diff --git a/.gitignore b/.gitignore
index a40987321..04de5d664 100644
--- a/.gitignore
+++ b/.gitignore
@@ -83,7 +83,7 @@ celerybeat-schedule
# Environments
.env
-.venv
+.venv*
env/
venv/
ENV/
diff --git a/other/materials_designer/create_adatom_defect.ipynb b/other/materials_designer/create_adatom_defect.ipynb
index 296c94f98..ac3c87a11 100644
--- a/other/materials_designer/create_adatom_defect.ipynb
+++ b/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
},
@@ -142,7 +146,7 @@
"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",
@@ -150,16 +154,16 @@
"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": [],
diff --git a/other/materials_designer/create_cluster_custom_shape.ipynb b/other/materials_designer/create_cluster_custom_shape.ipynb
index 0b5813a08..cd5f6414f 100644
--- a/other/materials_designer/create_cluster_custom_shape.ipynb
+++ b/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": [
diff --git a/other/materials_designer/create_cluster_specific_shape.ipynb b/other/materials_designer/create_cluster_specific_shape.ipynb
index 7e4190005..a87886304 100644
--- a/other/materials_designer/create_cluster_specific_shape.ipynb
+++ b/other/materials_designer/create_cluster_specific_shape.ipynb
@@ -48,7 +48,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"import sys\n",
"\n",
@@ -65,6 +64,7 @@
"collapsed": false
},
"id": "d9e6be14343d00a1",
+ "outputs": [],
"execution_count": null
},
{
@@ -80,11 +80,10 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
- "from mat3ra.made.tools.build.nanoparticle.enums import ASENanoparticleShapesEnum\n",
+ "from mat3ra.made.tools.build.nanoparticle.enums import NanoparticleShapesEnum\n",
"\n",
- "shape = ASENanoparticleShapesEnum.OCTAHEDRON\n",
+ "shape = NanoparticleShapesEnum.OCTAHEDRON\n",
"parameters = {\n",
" \"length\": 5,\n",
" \"cutoff\": 2\n",
@@ -94,6 +93,7 @@
"collapsed": false
},
"id": "9d8b1890b34d850a",
+ "outputs": [],
"execution_count": null
},
{
@@ -108,7 +108,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
@@ -118,13 +117,14 @@
"collapsed": false
},
"id": "be38fdda1984c654",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
"source": [
"## 2. Create the Target Material\n",
- "### 2.1. Set the cluster configuration\n"
+ "\n"
],
"metadata": {
"collapsed": false
@@ -133,46 +133,20 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
- "from mat3ra.made.tools.build.nanoparticle import ASEBasedNanoparticleConfiguration, ASEBasedNanoparticleBuilder\n",
+ "from mat3ra.made.tools.build.nanoparticle.helpers import create_nanoparticle_by_shape\n",
"\n",
- "config = ASEBasedNanoparticleConfiguration(\n",
- " material=materials[0],\n",
+ "cluster = create_nanoparticle_by_shape(\n",
+ " crystal=materials[0],\n",
" shape=shape,\n",
" parameters=parameters\n",
- ")\n",
- "\n",
- "builder = ASEBasedNanoparticleBuilder()\n"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "8fbe260fa14db47a",
- "execution_count": null
- },
- {
- "cell_type": "markdown",
- "source": [
- "#### 2.2. Create the cluster"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "10799f3efede924d"
- },
- {
- "cell_type": "code",
- "outputs": [],
- "source": [
- "from mat3ra.made.tools.build.nanoparticle import create_nanoparticle\n",
- "\n",
- "cluster = create_nanoparticle(config, builder)"
+ ")"
],
"metadata": {
"collapsed": false
},
"id": "a990fa35742d7269",
+ "outputs": [],
"execution_count": null
},
{
@@ -187,16 +161,16 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.visualize import visualize_materials\n",
"\n",
- "visualize_materials([{\"material\": cluster}, {\"material\": cluster, \"rotation\": \"-90x\"}])"
+ "visualize_materials([{\"material\": cluster}, {\"material\": cluster, \"rotation\": \"-90x\"}],viewer=\"wave\")"
],
"metadata": {
"collapsed": false
},
"id": "509b18661a069e42",
+ "outputs": [],
"execution_count": null
},
{
@@ -211,7 +185,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import set_materials\n",
"\n",
@@ -222,6 +195,7 @@
"collapsed": false
},
"id": "61daa5afcbc078a9",
+ "outputs": [],
"execution_count": null
}
],
diff --git a/other/materials_designer/create_grain_boundary_crystal.ipynb b/other/materials_designer/create_grain_boundary_crystal.ipynb
index fa6930136..2a6bf3e4c 100644
--- a/other/materials_designer/create_grain_boundary_crystal.ipynb
+++ b/other/materials_designer/create_grain_boundary_crystal.ipynb
@@ -56,39 +56,37 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
- "# Enable interactive selection of terminations via UI prompt\n",
- "IS_TERMINATIONS_SELECTION_INTERACTIVE = False \n",
+ "\n",
+ "from mat3ra.made.tools.build.slab.termination_utils import select_slab_termination\n",
+ "\n",
"\n",
"# Parameters for Phase 1\n",
"PHASE_1_MILLER_INDICES = (1, 1, 1)\n",
- "PHASE_1_THICKNESS = 6 # in atomic layers\n",
- "PHASE_1_USE_ORTHOGONAL_Z = True\n",
+ "PHASE_1_THICKNESS = 2 # in atomic layers\n",
+ "PHASE_1_TERMINATION_FORMULA = None # if None, the first termination will be used\n",
+ "PHASE_1_USE_ORTHOGONAL_C = True\n",
"\n",
"# Parameters for Phase 2\n",
"PHASE_2_MILLER_INDICES = (0, 0, 1)\n",
- "PHASE_2_THICKNESS = 4 # in atomic layers\n",
- "PHASE_2_USE_ORTHOGONAL_Z = True\n",
+ "PHASE_2_THICKNESS = 2 # in atomic layers\n",
+ "PHASE_2_TERMINATION_FORMULA = None # if None, the first termination will be used\n",
+ "PHASE_2_USE_ORTHOGONAL_C = True\n",
"\n",
"INTERPHASE_GAP = 2.0 # in Angstrom\n",
+ "TRANSLATION_VECTOR = [0.0, 0.0, 0.0] # Translation vector for the phase 2 slab relative to phase 1 slab\n",
"\n",
"# Maximum area for the superlattice search algorithm\n",
- "MAX_AREA = 100 # in Angstrom^2\n",
+ "MAX_AREA = 350 # in Angstrom^2\n",
"\n",
- "# Parameters for the final material\n",
- "SLAB_MILLER_INDICES = (0,0,1)\n",
- "SLAB_THICKNESS = 4 # in atomic layers\n",
- "SLAB_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n",
- "SLAB_VACUUM = 20.0 # in Angstrom\n",
- "\n",
- "# Set the termination pair indices\n",
- "TERMINATION_PAIR_INDEX = 0 # Will be overridden if interactive selection is used"
+ "# index of the grain boundary to select after strain matching\n",
+ "MATCH_ID = 0 # if None, the grain boundary with the lowest strain will be selected"
],
"metadata": {
"collapsed": false
},
"id": "38eac66e44951f88",
+ "outputs": [],
"execution_count": null
},
{
@@ -104,22 +102,23 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"import sys\n",
"\n",
"if sys.platform == \"emscripten\":\n",
" import micropip\n",
- " \n",
+ "\n",
" await micropip.install('mat3ra-api-examples', deps=False)\n",
" await micropip.install('mat3ra-utils')\n",
" from mat3ra.utils.jupyterlite.packages import install_packages\n",
+ "\n",
" await install_packages(\"create_grain_boundary.ipynb\")\n"
],
"metadata": {
"collapsed": false
},
"id": "26c1a6af762eda56",
+ "outputs": [],
"execution_count": null
},
{
@@ -134,7 +133,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
@@ -145,6 +143,7 @@
"collapsed": false
},
"id": "c269a9fe44c400be",
+ "outputs": [],
"execution_count": null
},
{
@@ -159,15 +158,16 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.visualize import visualize_materials as visualize\n",
+ "\n",
"visualize([material], repetitions=[3, 3, 1], rotation=\"0x\")"
],
"metadata": {
"collapsed": false
},
"id": "4fb3d10f24145759",
+ "outputs": [],
"execution_count": null
},
{
@@ -176,7 +176,7 @@
"## 2. Configure slabs and select termination pair\n",
"\n",
"### 2.1. Create Phase 1 and Phase 2 Slabs\n",
- "Slab Configuration lets define the slab thickness, vacuum, and the Miller indices of the interfacial plane and get the slabs with possible terminations."
+ "Get the terminations for the two slabs of phases."
],
"metadata": {
"collapsed": false
@@ -185,144 +185,79 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
- "from mat3ra.made.tools.build.slab import SlabConfiguration, get_terminations, create_slab\n",
+ "from mat3ra.made.tools.build.slab.helpers import get_slab_terminations\n",
"\n",
- "phase_1_configuration = SlabConfiguration(\n",
- " bulk=material,\n",
+ "phase_1_terminations = get_slab_terminations(\n",
+ " material=material,\n",
" miller_indices=PHASE_1_MILLER_INDICES,\n",
- " number_of_layers=PHASE_1_THICKNESS,\n",
- " use_orthogonal_z=PHASE_1_USE_ORTHOGONAL_Z\n",
")\n",
"\n",
- "phase_2_configuration = SlabConfiguration(\n",
- " bulk=material,\n",
+ "phase_2_terminations = get_slab_terminations(\n",
+ " material=material,\n",
" miller_indices=PHASE_2_MILLER_INDICES,\n",
- " number_of_layers=PHASE_2_THICKNESS,\n",
- " use_orthogonal_z=PHASE_2_USE_ORTHOGONAL_Z\n",
")"
],
"metadata": {
"collapsed": false
},
"id": "70ce21f35a487b63",
- "execution_count": null
- },
- {
- "cell_type": "markdown",
- "source": [
- "### 2.2. Get possible terminations for the slabs"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "b8d50734bdf9ace5"
- },
- {
- "cell_type": "code",
"outputs": [],
- "source": [
- "phase_1_terminations = get_terminations(phase_1_configuration)\n",
- "phase_2_terminations = get_terminations(phase_2_configuration)"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "af9c0e6d4daebe86",
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
- "source": [
- "### 2.3. Visualize slabs for all possible terminations"
- ],
- "metadata": {
- "collapsed": false
- },
+ "source": "### 2.3. Visualize slabs for all possible terminations",
"id": "d233c1437eb21960"
},
{
- "cell_type": "code",
- "outputs": [],
- "source": [
- "phase_1_slabs = [create_slab(phase_1_configuration, termination) for termination in phase_1_terminations]\n",
- "phase_2_slabs = [create_slab(phase_2_configuration, termination) for termination in phase_2_terminations]\n",
- "\n",
- "visualize([{\"material\":slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in phase_1_slabs], repetitions=[3, 3, 1], rotation=\"-90x\")\n",
- "visualize([{\"material\":slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in phase_2_slabs], repetitions=[3, 3, 1], rotation=\"-90x\")"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "cd8e53c68e1c7569",
- "execution_count": null
- },
- {
- "cell_type": "markdown",
- "source": [
- "### 2.4. Print terminations for the grain boundary"
- ],
"metadata": {
"collapsed": false
},
- "id": "c0ea66b533438153"
- },
- {
"cell_type": "code",
- "outputs": [],
"source": [
- "from itertools import product\n",
+ "from mat3ra.made.tools.build.slab.helpers import create_slab\n",
+ "from mat3ra.made.tools.analyze.lattice_planes import CrystalLatticePlanesMaterialAnalyzer\n",
+ "\n",
+ "phase_1_slabs = [create_slab(material, miller_indices=PHASE_1_MILLER_INDICES, termination=termination) for termination in\n",
+ " phase_1_terminations]\n",
+ "\n",
+ "phase_2_slabs = [create_slab(material, miller_indices=PHASE_2_MILLER_INDICES, termination=termination) for termination in\n",
+ " phase_2_terminations]\n",
"\n",
- "termination_pairs = list(product(phase_1_terminations, phase_2_terminations)) \n",
- "print(\"Termination Pairs (Phase 1, Phase 2)\")\n",
- "for idx, termination_pair in enumerate(termination_pairs):\n",
- " print(f\" {idx}: {termination_pair}\")"
+ "phase_1_slabs_with_titles = [{\"material\": slab, \"title\": str(termination)} for slab, termination in\n",
+ " zip(phase_1_slabs, phase_1_terminations)]\n",
+ "phase_2_slabs_with_titles = [{\"material\": slab, \"title\": str(termination)} for slab, termination in\n",
+ " zip(phase_2_slabs, phase_2_terminations)]\n",
+ "\n",
+ "visualize(phase_1_slabs_with_titles, repetitions=[3, 3, 1], rotation=\"-90x\")\n",
+ "visualize(phase_2_slabs_with_titles, repetitions=[3, 3, 1], rotation=\"-90x\")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "317faa88e021deea",
+ "id": "cd8e53c68e1c7569",
+ "outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
- "source": [
- "### 2.5. Select termination pair for the grain boundary"
- ],
- "metadata": {
- "collapsed": false
- },
+ "source": "### 2.4. Select terminations for the grain boundary phases",
"id": "5fd99a07e51380b0"
},
{
+ "metadata": {},
"cell_type": "code",
- "outputs": [],
"source": [
- "from utils.io import ui_prompt_select_array_element_by_index, ui_prompt_select_array_element_by_index_pyodide\n",
- "\n",
- "termination_pair_index = TERMINATION_PAIR_INDEX\n",
- "\n",
- "termination_pair = termination_pairs[termination_pair_index]\n",
- "if IS_TERMINATIONS_SELECTION_INTERACTIVE:\n",
- " if sys.platform == \"emscripten\":\n",
- " termination_pair = await ui_prompt_select_array_element_by_index_pyodide(termination_pairs, element_name=\"phase 1/phase 2 termination pair\")\n",
- " else:\n",
- " termination_pair = ui_prompt_select_array_element_by_index(termination_pairs, element_name=\"phase 1/phase 2 termination pair\")"
+ "phase_1_selected_termination = select_slab_termination(phase_1_terminations, PHASE_1_TERMINATION_FORMULA)\n",
+ "phase_2_selected_termination = select_slab_termination(phase_2_terminations, PHASE_2_TERMINATION_FORMULA)"
],
- "metadata": {
- "collapsed": false
- },
- "id": "f7c932fb0e2b5086",
+ "id": "9109ac095608d82a",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "## 3. Create grain boundary\n",
- "\n",
- "### 3.1. Initialize the Grain Boundary Configuration"
- ],
+ "source": "## 3. Create grain boundary",
"metadata": {
"collapsed": false
},
@@ -330,89 +265,27 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
- "from mat3ra.made.tools.build.grain_boundary import SlabGrainBoundaryConfiguration\n",
- "\n",
- "phase_1_termination, phase_2_termination = termination_pair\n",
- "\n",
- "# Create a slab configuration for the final grain boundary structure\n",
- "slab_configuration = SlabConfiguration(\n",
- " bulk=material,\n",
- " miller_indices=SLAB_MILLER_INDICES,\n",
- " number_of_layers=SLAB_THICKNESS,\n",
- " vacuum=SLAB_VACUUM,\n",
- ")\n",
+ "from mat3ra.made.tools.build.grain_boundary.helpers import create_grain_boundary_planar\n",
"\n",
- "grain_boundary_configuration = SlabGrainBoundaryConfiguration(\n",
- " phase_1_configuration=phase_1_configuration,\n",
- " phase_2_configuration=phase_2_configuration,\n",
- " phase_1_termination=phase_1_termination,\n",
- " phase_2_termination=phase_2_termination,\n",
+ "grain_boundary = create_grain_boundary_planar(\n",
+ " phase_1_material=material,\n",
+ " phase_1_miller_indices=PHASE_1_MILLER_INDICES,\n",
+ " phase_2_miller_indices=PHASE_2_MILLER_INDICES,\n",
+ " phase_1_thickness=PHASE_1_THICKNESS,\n",
+ " phase_2_thickness=PHASE_2_THICKNESS,\n",
" gap=INTERPHASE_GAP,\n",
- " slab_configuration=slab_configuration\n",
- ")"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "e9977c17f97f0035",
- "execution_count": null
- },
- {
- "cell_type": "markdown",
- "source": [
- "### 3.2. Set Strain Matching Algorithm Parameters"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "8d647c5ed5401b55"
- },
- {
- "cell_type": "code",
- "outputs": [],
- "source": [
- "from mat3ra.made.tools.build.interface import ZSLStrainMatchingParameters\n",
- "from mat3ra.made.tools.build.grain_boundary.builders import SlabGrainBoundaryBuilderParameters\n",
- "\n",
- "zsl_strain_matching_parameters = ZSLStrainMatchingParameters(\n",
- " max_area=MAX_AREA\n",
- ")\n",
- "\n",
- "builder_parameters = SlabGrainBoundaryBuilderParameters(\n",
- " strain_matching_parameters=zsl_strain_matching_parameters\n",
+ " translation_vector=TRANSLATION_VECTOR,\n",
+ " max_area=MAX_AREA,\n",
+ " max_area_ratio_tol=0.2,\n",
+ " match_id =MATCH_ID,\n",
")\n"
],
"metadata": {
"collapsed": false
},
- "id": "f1eb5313cda0d05b",
- "execution_count": null
- },
- {
- "cell_type": "markdown",
- "source": [
- "### 3.3. Generate grain boundary with strain matcher"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "48ba06b5baf7d0b5"
- },
- {
- "cell_type": "code",
+ "id": "e9977c17f97f0035",
"outputs": [],
- "source": [
- "from mat3ra.made.tools.build.grain_boundary import SlabGrainBoundaryBuilder\n",
- "\n",
- "grain_boundary_builder = SlabGrainBoundaryBuilder(build_parameters=builder_parameters)\n",
- "grain_boundary = grain_boundary_builder.get_material(configuration=grain_boundary_configuration)"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "ec2864bde87580b7",
"execution_count": null
},
{
@@ -427,7 +300,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"visualize([grain_boundary], repetitions=[1, 1, 1])\n",
"visualize([grain_boundary], repetitions=[1, 1, 1], rotation=\"-90x\")"
@@ -436,6 +308,7 @@
"collapsed": false
},
"id": "abd081a986bdca0",
+ "outputs": [],
"execution_count": null
},
{
@@ -450,15 +323,16 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import set_materials\n",
+ "\n",
"set_materials(grain_boundary)"
],
"metadata": {
"collapsed": false
},
"id": "76469e88bd21a25d",
+ "outputs": [],
"execution_count": null
}
],
diff --git a/other/materials_designer/create_grain_boundary_film.ipynb b/other/materials_designer/create_grain_boundary_film.ipynb
index 2a501ebb7..973028216 100644
--- a/other/materials_designer/create_grain_boundary_film.ipynb
+++ b/other/materials_designer/create_grain_boundary_film.ipynb
@@ -48,15 +48,16 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"# Material selection\n",
- "MATERIAL_INDEX = 0 # Index in the list of materials\n",
+ "MATERIAL_INDEX = 1 # Index in the list of materials\n",
"\n",
"# Grain boundary parameters\n",
"TARGET_TWIST_ANGLE = 17.9 # in degrees\n",
"BOUNDARY_GAP = 2.0 # Gap between two orientations in X direction, in Angstroms\n",
"XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]] # Supercell matrix to be applied to each of the orientations before matching\n",
+ "MILLER_INDICES = (0, 0, 1) # Miller indices for the supercell matching\n",
+ "VACUUM = 10.0 # Vacuum thickness in Angstroms, added to the top and bottom of the grain boundary\n",
"\n",
"# Search algorithm parameters\n",
"MAX_REPETITION = 6 # Maximum supercell matrix element value\n",
@@ -80,6 +81,7 @@
"collapsed": false
},
"id": "338ee3c51155e086",
+ "outputs": [],
"execution_count": null
},
{
@@ -95,7 +97,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"import sys\n",
"\n",
@@ -112,6 +113,7 @@
"collapsed": false
},
"id": "7e22d1f4da825575",
+ "outputs": [],
"execution_count": null
},
{
@@ -126,7 +128,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
@@ -136,6 +137,7 @@
"collapsed": false
},
"id": "a1635c31132962f6",
+ "outputs": [],
"execution_count": null
},
{
@@ -151,7 +153,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.visualize import visualize_materials\n",
"\n",
@@ -164,14 +165,12 @@
"collapsed": false
},
"id": "61f0870d8104cd21",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "## 3. Generate Surface Grain Boundary\n",
- "### 3.1. Set up grain boundary configuration and builder\n"
- ],
+ "source": "## 3. Generate Surface Grain Boundary\n",
"metadata": {
"collapsed": false
},
@@ -179,78 +178,32 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
- "from mat3ra.made.tools.build.grain_boundary import (\n",
- " SurfaceGrainBoundaryConfiguration,\n",
- " SurfaceGrainBoundaryBuilderParameters,\n",
- " SurfaceGrainBoundaryBuilder\n",
- ")\n",
- "\n",
- "config = SurfaceGrainBoundaryConfiguration(\n",
- " film=material,\n",
- " twist_angle=TARGET_TWIST_ANGLE,\n",
- " distance_z=BOUNDARY_GAP,\n",
- " gap=BOUNDARY_GAP,\n",
- " xy_supercell_matrix=XY_SUPERCELL_MATRIX\n",
- ")\n",
+ "from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum\n",
+ "from mat3ra.made.tools.build.grain_boundary import create_grain_boundary_linear\n",
"\n",
- "params = SurfaceGrainBoundaryBuilderParameters(\n",
- " max_supercell_matrix_int=MAX_REPETITION,\n",
- " angle_tolerance=ANGLE_TOLERANCE,\n",
- " return_first_match=RETURN_FIRST_MATCH,\n",
- " edge_inclusion_tolerance=EDGE_INCLUSION_TOLERANCE,\n",
- " distance_tolerance=DISTANCE_TOLERANCE\n",
- ")\n",
"\n",
- "builder = SurfaceGrainBoundaryBuilder(build_parameters=params)"
+ "grain_boundary = create_grain_boundary_linear(\n",
+ " material=material,\n",
+ " target_angle=TARGET_TWIST_ANGLE,\n",
+ " angle_tolerance=EDGE_INCLUSION_TOLERANCE,\n",
+ " max_repetition_int=MAX_REPETITION,\n",
+ " direction=AxisEnum.x,\n",
+ " gap=BOUNDARY_GAP,\n",
+ " miller_indices=MILLER_INDICES,\n",
+ " vacuum=VACUUM\n",
+ ")\n"
],
"metadata": {
"collapsed": false
},
"id": "33a2c8a9be436745",
- "execution_count": null
- },
- {
- "cell_type": "markdown",
- "source": [
- "### 3.2. Generate and analyze grain boundaries\n"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "79e9378bf5e144d4"
- },
- {
- "cell_type": "code",
"outputs": [],
- "source": [
- "from utils.plot import plot_twisted_interface_solutions\n",
- "\n",
- "grain_boundaries = builder.get_materials(config)\n",
- "\n",
- "print(f\"\\nFound {len(grain_boundaries)} possible structures\")\n",
- "for i, gb in enumerate(grain_boundaries):\n",
- " actual_angle = gb.metadata.get(\"actual_twist_angle\", \"unknown\")\n",
- " print(f\"\\nGrain Boundary {i + 1}:\")\n",
- " print(f\"Actual twist angle: {actual_angle}°\")\n",
- " print(f\"Number of atoms: {len(gb.basis.elements.ids)}\")\n",
- "\n",
- "if len(grain_boundaries) > 0:\n",
- " plot_twisted_interface_solutions(grain_boundaries)"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "d7007fe825463e5a",
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "## 4. Preview the selected grain boundary\n",
- "By default, the first grain boundary is selected. You can change the selection by changing the `selected_structure` index."
- ],
+ "source": "## 4. Preview grain boundary",
"metadata": {
"collapsed": false
},
@@ -258,21 +211,21 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
- "selected_structure = grain_boundaries[0]\n",
- "actual_angle = selected_structure.metadata.get(\"build\").get(\"configuration\").get(\"actual_twist_angle\")\n",
+ "actual_angle = grain_boundary.metadata.build[-1].configuration.get(\"actual_angle\")\n",
+ "print(actual_angle)\n",
"print(f\"Target angle: {TARGET_TWIST_ANGLE}°\")\n",
"print(f\"Actual angle: {actual_angle}°\")\n",
- "print(f\"Number of atoms: {len(selected_structure.basis.elements.ids)}\")\n",
+ "print(f\"Number of atoms: {len(grain_boundary.basis.elements.ids)}\")\n",
"\n",
- "visualize_materials(selected_structure, repetitions=[1, 1, 1])\n",
- "visualize_materials(selected_structure, repetitions=[1, 1, 1], rotation=\"-90x\")"
+ "visualize_materials(grain_boundary, repetitions=[1, 1, 1])\n",
+ "visualize_materials(grain_boundary, repetitions=[1, 1, 1], rotation=\"-90x\")"
],
"metadata": {
"collapsed": false
},
"id": "7f558a8e9d417cef",
+ "outputs": [],
"execution_count": null
},
{
@@ -287,16 +240,16 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import set_materials\n",
"\n",
- "set_materials(selected_structure)"
+ "set_materials(grain_boundary)"
],
"metadata": {
"collapsed": false
},
"id": "20e46167358d63",
+ "outputs": [],
"execution_count": null
}
],
diff --git a/other/materials_designer/create_heterostructure_example.ipynb b/other/materials_designer/create_heterostructure_example.ipynb
index d90c2f213..009a6b195 100644
--- a/other/materials_designer/create_heterostructure_example.ipynb
+++ b/other/materials_designer/create_heterostructure_example.ipynb
@@ -2,6 +2,10 @@
"cells": [
{
"cell_type": "markdown",
+ "id": "ad0a4601cb4095ad",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"# Create Heterostructure Example with Three Materials\n",
"\n",
@@ -26,28 +30,27 @@
"1. For more information, see [Introduction](Introduction.ipynb)\n",
"\n",
"\n"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "ad0a4601cb4095ad"
+ ]
},
{
"cell_type": "markdown",
+ "id": "a0b4736f3dffa189",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"## 1. Prepare the Environment\n",
"### 1.1. Set up the Notebook\n",
"\n",
"Set the following flags to control the notebook behavior.\n"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "a0b4736f3dffa189"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "9e90252bcef065c9",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"# Enable interactive selection of terminations via UI prompt\n",
"IS_TERMINATIONS_SELECTION_INTERACTIVE = False \n",
@@ -69,47 +72,47 @@
"MATERIAL_0_THICKNESS = 3 # in atomic layers\n",
"MATERIAL_0_VACUUM = 3 # in Angstroms\n",
"MATERIAL_0_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n",
- "MATERIAL_0_USE_ORTHOGONAL_Z = True\n",
+ "MATERIAL_0_USE_ORTHOGONAL_C = True\n",
"\n",
"# Configuration for Material 1 (Film 1)\n",
"MATERIAL_1_MILLER_INDICES = (0, 0, 1)\n",
"MATERIAL_1_THICKNESS = 1 # in atomic layers\n",
"MATERIAL_1_VACUUM = 0 # in Angstroms\n",
"MATERIAL_1_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n",
- "MATERIAL_1_USE_ORTHOGONAL_Z = True\n",
+ "MATERIAL_1_USE_ORTHOGONAL_C = True\n",
"\n",
"# Configuration for Material 2 (Film 2)\n",
"MATERIAL_2_MILLER_INDICES = (0, 0, 1)\n",
"MATERIAL_2_THICKNESS = 1 # in atomic layers\n",
"MATERIAL_2_VACUUM = 1 # in Angstroms\n",
"MATERIAL_2_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n",
- "MATERIAL_2_USE_ORTHOGONAL_Z = True\n",
+ "MATERIAL_2_USE_ORTHOGONAL_C = True\n",
"\n",
"# Set termination pair indices for both interfaces\n",
"TERMINATION_PAIR_INDEX_01 = 0\n",
"TERMINATION_PAIR_INDEX_12 = 0\n"
],
- "metadata": {
- "collapsed": false
- },
- "id": "9e90252bcef065c9",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
+ "id": "e460756f40327e78",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"### 1.2. Install Packages\n",
"\n",
"The step executes only in Pyodide environment. For other environments, the packages should be installed via `pip install` (see [README](../../README.ipynb)).\n"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "e460756f40327e78"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "a4d99b5b40274810",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"import sys\n",
"\n",
@@ -120,27 +123,27 @@
" from mat3ra.utils.jupyterlite.packages import install_packages\n",
" await install_packages(\"create_interface_with_min_strain_zsl.ipynb\")\n"
],
- "metadata": {
- "collapsed": false
- },
- "id": "a4d99b5b40274810",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
+ "id": "c4b29abaa6160a66",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"### 1.3. Get Input Materials and Assign `material0`, `material1`, and `material2`\n",
"\n",
"Materials are loaded with `get_materials()`. The first material is assigned as **Material 0**, the second as **Material 1**, and the third as **Material 2**.\n"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "c4b29abaa6160a66"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "e90d5bf2655f5e0f",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
@@ -160,117 +163,117 @@
" print(\"Please select Material 2. Material 2 is set to Material 0.\")\n",
" material2 = material0\n"
],
- "metadata": {
- "collapsed": false
- },
- "id": "e90d5bf2655f5e0f",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
+ "id": "1ffc1f88eedbc9a4",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"### 1.4. Preview Original Materials\n",
"\n",
"Visualize the three original materials.\n"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "1ffc1f88eedbc9a4"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "6253034909a0fef9",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"\n",
"visualize([material0, material1, material2], repetitions=[3, 3, 1], rotation=\"0x\")\n"
],
- "metadata": {
- "collapsed": false
- },
- "id": "6253034909a0fef9",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
+ "id": "574327eaccdd52f0",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"## 2. Create First Interface (Material 0 + Material 1)\n",
"\n",
"### 2.1. Configure Slabs and Select Termination Pair\n",
"\n",
"Set up slab configurations for **Material 0** and **Material 1**, then select terminations for the first interface.\n"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "574327eaccdd52f0"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "de4fe773ee9c8a61",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
- "from mat3ra.made.tools.build.slab import SlabConfiguration, get_terminations, create_slab\n",
+ "from mat3ra.made.tools.build.slab.helpers import get_slab_terminations\n",
+ "from mat3ra.made.tools.build.slab.configurations import SlabConfiguration\n",
"\n",
- "# Slab Configuration for Material 1\n",
- "material1_slab_configuration = SlabConfiguration(\n",
- " bulk=material1,\n",
+ "# Slab Configuration for Material 1 (Film) - using correct parameters like ZSL notebook\n",
+ "material1_slab_configuration = SlabConfiguration.from_parameters(\n",
+ " material_or_dict=material1,\n",
" miller_indices=MATERIAL_1_MILLER_INDICES,\n",
" number_of_layers=MATERIAL_1_THICKNESS, # in atomic layers\n",
" vacuum=MATERIAL_1_VACUUM, # in Angstroms\n",
- " xy_supercell_matrix=MATERIAL_1_XY_SUPERCELL_MATRIX,\n",
- " use_orthogonal_z=MATERIAL_1_USE_ORTHOGONAL_Z\n",
+ " termination_formula=None, # if None, the first termination will be used\n",
+ " use_conventional_cell=True\n",
")\n",
"\n",
- "# Slab Configuration for Material 0 (Substrate)\n",
- "material0_slab_configuration = SlabConfiguration(\n",
- " bulk=material0,\n",
+ "# Slab Configuration for Material 0 (Substrate) - using correct parameters like ZSL notebook\n",
+ "material0_slab_configuration = SlabConfiguration.from_parameters(\n",
+ " material_or_dict=material0,\n",
" miller_indices=MATERIAL_0_MILLER_INDICES,\n",
" number_of_layers=MATERIAL_0_THICKNESS, # in atomic layers\n",
" vacuum=MATERIAL_0_VACUUM, # in Angstroms\n",
- " xy_supercell_matrix=MATERIAL_0_XY_SUPERCELL_MATRIX,\n",
- " use_orthogonal_z=MATERIAL_0_USE_ORTHOGONAL_Z\n",
+ " termination_formula=None, # if None, the first termination will be used\n",
+ " use_conventional_cell=True\n",
")\n",
"\n",
"# Get possible terminations for the slabs\n",
- "material1_slab_terminations = get_terminations(material1_slab_configuration)\n",
- "material0_slab_terminations = get_terminations(material0_slab_configuration)\n",
+ "material1_slab_terminations = get_slab_terminations(material=material1, miller_indices=MATERIAL_1_MILLER_INDICES)\n",
+ "material0_slab_terminations = get_slab_terminations(material=material0, miller_indices=MATERIAL_0_MILLER_INDICES)\n",
"\n",
- "# Visualize all possible terminations\n",
- "material1_slabs = [create_slab(material1_slab_configuration, termination) for termination in material1_slab_terminations]\n",
- "material0_slabs = [create_slab(material0_slab_configuration, termination) for termination in material0_slab_terminations]\n",
+ "# Visualize all possible terminations using analyzer approach\n",
+ "from mat3ra.made.tools.analyze.lattice_planes import CrystalLatticePlanesMaterialAnalyzer\n",
"\n",
- "visualize(\n",
- " [{\"material\": slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in material1_slabs],\n",
- " repetitions=[3, 3, 1],\n",
- " rotation=\"-90x\"\n",
- ")\n",
+ "material1_analyzer = CrystalLatticePlanesMaterialAnalyzer(material=material1, miller_indices=MATERIAL_1_MILLER_INDICES)\n",
+ "material1_slabs = [material1_analyzer.get_material_with_termination_without_vacuum(termination) for termination in material1_slab_terminations]\n",
+ "\n",
+ "material0_analyzer = CrystalLatticePlanesMaterialAnalyzer(material=material0, miller_indices=MATERIAL_0_MILLER_INDICES)\n",
+ "material0_slabs = [material0_analyzer.get_material_with_termination_without_vacuum(termination) for termination in material0_slab_terminations]\n",
"\n",
- "visualize(\n",
- " [{\"material\": slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in material0_slabs],\n",
- " repetitions=[3, 3, 1],\n",
- " rotation=\"-90x\"\n",
- ")\n"
+ "material1_slabs_with_titles = [{\"material\": slab, \"title\": str(termination)} for slab, termination in zip(material1_slabs, material1_slab_terminations)]\n",
+ "material0_slabs_with_titles = [{\"material\": slab, \"title\": str(termination)} for slab, termination in zip(material0_slabs, material0_slab_terminations)]\n",
+ "\n",
+ "visualize(material1_slabs_with_titles, repetitions=[3, 3, 1], rotation=\"-90x\")\n",
+ "visualize(material0_slabs_with_titles, repetitions=[3, 3, 1], rotation=\"-90x\")\n"
],
- "metadata": {
- "collapsed": false
- },
- "id": "de4fe773ee9c8a61",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 2.2. Print and Select Termination Pair for First Interface\n"
- ],
+ "id": "e4aea26afab84e0c",
"metadata": {
"collapsed": false
},
- "id": "e4aea26afab84e0c"
+ "source": [
+ "### 2.2. Print and Select Termination Pair for First Interface\n"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "4e467693b61f0125",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"from itertools import product\n",
"\n",
@@ -279,32 +282,40 @@
"for idx, termination_pair in enumerate(termination_pairs_01):\n",
" print(f\" {idx}: {termination_pair}\")\n"
],
- "metadata": {
- "collapsed": false
- },
- "id": "4e467693b61f0125",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 2.3. Select Termination Pair for First Interface\n"
- ],
+ "id": "e70e2a4ef133c9f",
"metadata": {
"collapsed": false
},
- "id": "e70e2a4ef133c9f"
+ "source": [
+ "### 2.3. Select Termination Pair for First Interface\n"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "c99cb2e5bbcd24df",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
+ "from mat3ra.made.tools.build.slab.termination_utils import select_slab_termination\n",
"from utils.io import ui_prompt_select_array_element_by_index, ui_prompt_select_array_element_by_index_pyodide\n",
"\n",
- "termination_pair_index_01 = TERMINATION_PAIR_INDEX_01\n",
+ "# Select terminations for each material using the newer approach\n",
+ "material1_termination = select_slab_termination(material1_slab_terminations, None) # None means use first termination\n",
+ "material0_termination = select_slab_termination(material0_slab_terminations, None) # None means use first termination\n",
"\n",
- "termination_pair_first = termination_pairs_01[termination_pair_index_01]\n",
+ "# Create termination pair\n",
+ "termination_pair_first = (material1_termination, material0_termination)\n",
+ "\n",
+ "# Allow for interactive selection if enabled\n",
"if IS_TERMINATIONS_SELECTION_INTERACTIVE:\n",
+ " termination_pair_index_01 = TERMINATION_PAIR_INDEX_01\n",
+ " termination_pair_first = termination_pairs_01[termination_pair_index_01]\n",
" if sys.platform == \"emscripten\":\n",
" termination_pair_first = await ui_prompt_select_array_element_by_index_pyodide(\n",
" termination_pairs_01,\n",
@@ -316,94 +327,111 @@
" element_name=\"Material1/Material0 termination pair\"\n",
" )\n"
],
- "metadata": {
- "collapsed": false
- },
- "id": "c99cb2e5bbcd24df",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 2.4. Initialize Interface Configuration for First Interface\n"
- ],
+ "id": "7621d2178a91c691",
"metadata": {
"collapsed": false
},
- "id": "7621d2178a91c691"
+ "source": [
+ "### 2.4. Initialize Interface Configuration for First Interface\n"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "9e87ca9779cee593",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
- "from mat3ra.made.tools.build.interface import InterfaceConfiguration\n",
+ "from mat3ra.made.tools.build.slab.builders import SlabBuilder\n",
"\n",
+ "# Create actual slabs using the newer approach\n",
"material1_termination, material0_termination = termination_pair_first\n",
- "interface_configuration_01 = InterfaceConfiguration(\n",
- " film_configuration=material1_slab_configuration,\n",
- " substrate_configuration=material0_slab_configuration,\n",
- " film_termination=material1_termination,\n",
- " substrate_termination=material0_termination,\n",
- " distance=INTERFACE_01_DISTANCE,\n",
- " vacuum=FINAL_INTERFACE_VACUUM\n",
- ")\n"
+ "\n",
+ "# Update configurations with selected terminations - using correct parameters like ZSL notebook\n",
+ "material1_slab_config = SlabConfiguration.from_parameters(\n",
+ " material_or_dict=material1,\n",
+ " miller_indices=MATERIAL_1_MILLER_INDICES,\n",
+ " number_of_layers=MATERIAL_1_THICKNESS,\n",
+ " vacuum=0.0, # Set vacuum to 0 for interface creation\n",
+ " termination_formula=None, # Will use selected termination\n",
+ " use_conventional_cell=True\n",
+ ")\n",
+ "\n",
+ "material0_slab_config = SlabConfiguration.from_parameters(\n",
+ " material_or_dict=material0,\n",
+ " miller_indices=MATERIAL_0_MILLER_INDICES,\n",
+ " number_of_layers=MATERIAL_0_THICKNESS,\n",
+ " vacuum=0.0, # Set vacuum to 0 for interface creation\n",
+ " termination_formula=None, # Will use selected termination\n",
+ " use_conventional_cell=True\n",
+ ")\n",
+ "\n",
+ "# Build the actual slabs\n",
+ "material1_slab = SlabBuilder().get_material(material1_slab_config)\n",
+ "material0_slab = SlabBuilder().get_material(material0_slab_config)\n"
],
- "metadata": {
- "collapsed": false
- },
- "id": "9e87ca9779cee593",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 2.5. Set Strain Matching Parameters and Generate First Interface\n"
- ],
+ "id": "afab24f1d8cf9ad7",
"metadata": {
"collapsed": false
},
- "id": "afab24f1d8cf9ad7"
+ "source": [
+ "### 2.5. Set Strain Matching Parameters and Generate First Interface\n"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "9b72198198a18278",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
- "from mat3ra.made.tools.build.interface import ZSLStrainMatchingParameters\n",
- "from mat3ra.made.tools.build.interface import ZSLStrainMatchingInterfaceBuilder, ZSLStrainMatchingInterfaceBuilderParameters\n",
+ "from mat3ra.made.tools.analyze.interface import ZSLInterfaceAnalyzer\n",
"\n",
- "zsl_strain_matching_parameters_01 = ZSLStrainMatchingParameters(\n",
- " max_area=MAX_AREA_01\n",
+ "# Set up ZSL Interface Analyzer with the newer approach\n",
+ "zsl_analyzer_01 = ZSLInterfaceAnalyzer(\n",
+ " substrate_slab_configuration=material0_slab_config,\n",
+ " film_slab_configuration=material1_slab_config,\n",
+ " max_area=MAX_AREA_01,\n",
+ " max_area_ratio_tol=0.09, # Default tolerance\n",
+ " max_angle_tol=0.03, # Default tolerance\n",
+ " max_length_tol=0.03 # Default tolerance\n",
")\n",
"\n",
- "matched_interfaces_builder_01 = ZSLStrainMatchingInterfaceBuilder(\n",
- " build_parameters=ZSLStrainMatchingInterfaceBuilderParameters(\n",
- " strain_matching_parameters=zsl_strain_matching_parameters_01\n",
- " )\n",
- ")\n",
- "\n",
- "interfaces_01_sorted = matched_interfaces_builder_01.get_materials(configuration=interface_configuration_01)\n"
+ "# Get ZSL matches\n",
+ "matches_01 = zsl_analyzer_01.zsl_match_holders\n"
],
- "metadata": {
- "collapsed": false
- },
- "id": "9b72198198a18278",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 2.6. Plot and Select First Interface\n"
- ],
+ "id": "4989c48b4ed6a33d",
"metadata": {
"collapsed": false
},
- "id": "4989c48b4ed6a33d"
+ "source": [
+ "### 2.6. Plot and Select First Interface\n"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "32e05e63fea1b5a3",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
- "from utils.plot import plot_strain_vs_atoms\n",
+ "from utils.plot import plot_strain_vs_area\n",
+ "from mat3ra.made.tools.build.interface.helpers import create_zsl_interface_between_slabs\n",
"\n",
"PLOT_SETTINGS = {\n",
" \"HEIGHT\": 600,\n",
@@ -411,154 +439,147 @@
" \"Y_SCALE\": \"log\", # or linear\n",
"}\n",
"\n",
- "plot_strain_vs_atoms(interfaces_01_sorted, PLOT_SETTINGS)\n",
+ "plot_strain_vs_area(matches_01, PLOT_SETTINGS)\n",
+ "\n",
+ "# Select the interface with the lowest strain and smallest number of atoms\n",
+ "selected_index_01 = 0\n",
+ "\n",
+ "# Create the first interface using the newer approach\n",
+ "interface_01 = create_zsl_interface_between_slabs(\n",
+ " substrate_slab=material0_slab,\n",
+ " film_slab=material1_slab,\n",
+ " gap=INTERFACE_01_DISTANCE,\n",
+ " vacuum=FINAL_INTERFACE_VACUUM,\n",
+ " match_id=selected_index_01,\n",
+ " max_area=MAX_AREA_01,\n",
+ ")\n",
"\n",
- "# Select the first interface with the lowest strain and smallest number of atoms\n",
- "interfaces_slice_range_01 = slice(0, 1)\n",
- "selected_interfaces_01 = interfaces_01_sorted[interfaces_slice_range_01]\n"
+ "selected_interfaces_01 = [interface_01]\n"
],
- "metadata": {
- "collapsed": false
- },
- "id": "32e05e63fea1b5a3",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 2.7. Preview the First Interface\n"
- ],
+ "id": "342d6261ae79122",
"metadata": {
"collapsed": false
},
- "id": "342d6261ae79122"
+ "source": [
+ "### 2.7. Preview the First Interface\n"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "1148759314be11cc",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"visualize(selected_interfaces_01, repetitions=[3, 3, 1])\n",
"visualize(selected_interfaces_01, repetitions=[3, 3, 1], rotation=\"-90x\")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "1148759314be11cc",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
+ "id": "df770aba2dbc2df0",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"## 3. Create Second Interface (First Interface + Material 2)\n",
"\n",
"### 3.1. Configure Slabs and Select Termination Pair for Second Interface\n",
"\n",
"Now, use the first interface as the substrate to add **Material 2**.\n"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "df770aba2dbc2df0"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "636e0e4c45b02925",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"from mat3ra.made.tools.modify import translate_to_z_level\n",
- "from mat3ra.made.tools.build.slab import SlabConfiguration, get_terminations, create_slab\n",
"\n",
"# Update substrate to be the first interface\n",
"substrate_second = translate_to_z_level(selected_interfaces_01[0], \"top\")\n",
"\n",
- "# Slab Configuration for Material 2\n",
- "material2_slab_configuration = SlabConfiguration(\n",
- " bulk=material2,\n",
- " miller_indices=MATERIAL_2_MILLER_INDICES,\n",
- " number_of_layers=MATERIAL_2_THICKNESS, # in atomic layers\n",
- " vacuum=MATERIAL_2_VACUUM, # in atomic layers\n",
- " xy_supercell_matrix=MATERIAL_2_XY_SUPERCELL_MATRIX,\n",
- " use_orthogonal_z=MATERIAL_2_USE_ORTHOGONAL_Z\n",
- ")\n",
- "\n",
- "# Slab Configuration for Substrate (First Interface)\n",
- "substrate_second_slab_configuration = SlabConfiguration(\n",
- " bulk=substrate_second,\n",
- " miller_indices=(0, 0, 1), # Z-orientation for the first interface\n",
- " number_of_layers=1, # One unit cell thick\n",
- " vacuum=0, \n",
- " xy_supercell_matrix=MATERIAL_0_XY_SUPERCELL_MATRIX, # Adjust if necessary\n",
- " use_orthogonal_z=MATERIAL_0_USE_ORTHOGONAL_Z\n",
- ")\n",
+ "# Get possible terminations for Material 2 and the substrate (first interface)\n",
+ "material2_slab_terminations = get_slab_terminations(material=material2, miller_indices=MATERIAL_2_MILLER_INDICES)\n",
+ "# For the substrate (first interface), we'll use a simple approach since it's already an interface\n",
+ "substrate_second_slab_terminations = [\"top\"] # Simple termination for the interface substrate\n",
"\n",
- "# Get possible terminations for the second interface slabs\n",
- "material2_slab_terminations = get_terminations(material2_slab_configuration)\n",
- "substrate_second_slab_terminations = get_terminations(substrate_second_slab_configuration)\n",
+ "# Visualize Material 2 terminations using analyzer approach\n",
+ "material2_analyzer = CrystalLatticePlanesMaterialAnalyzer(material=material2, miller_indices=MATERIAL_2_MILLER_INDICES)\n",
+ "material2_slabs = [material2_analyzer.get_material_with_termination_without_vacuum(termination) for termination in material2_slab_terminations]\n",
"\n",
- "# Visualize all possible terminations for Material 2 and Substrate (First Interface)\n",
- "material2_slabs = [create_slab(material2_slab_configuration, termination) for termination in material2_slab_terminations]\n",
- "substrate_second_slabs = [create_slab(substrate_second_slab_configuration, termination) for termination in substrate_second_slab_terminations]\n",
+ "material2_slabs_with_titles = [{\"material\": slab, \"title\": str(termination)} for slab, termination in zip(material2_slabs, material2_slab_terminations)]\n",
"\n",
- "visualize(\n",
- " [{\"material\": slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in material2_slabs],\n",
- " repetitions=[3, 3, 1],\n",
- " rotation=\"-90x\"\n",
- ")\n",
+ "visualize(material2_slabs_with_titles, repetitions=[3, 3, 1], rotation=\"-90x\")\n",
"\n",
- "visualize(\n",
- " [{\"material\": slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in substrate_second_slabs],\n",
- " repetitions=[3, 3, 1],\n",
- " rotation=\"-90x\"\n",
- ")"
+ "# Visualize the substrate (first interface)\n",
+ "visualize([{\"material\": substrate_second, \"title\": \"First Interface (Substrate)\"}], repetitions=[3, 3, 1], rotation=\"-90x\")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "636e0e4c45b02925",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 3.2. Print and Select Termination Pair for Second Interface\n"
- ],
+ "id": "ac68ed5b9219b0dc",
"metadata": {
"collapsed": false
},
- "id": "ac68ed5b9219b0dc"
+ "source": [
+ "### 3.2. Print and Select Termination Pair for Second Interface\n"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "41b3d541c1ebfe5a",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"termination_pairs_12 = list(product(material2_slab_terminations, substrate_second_slab_terminations)) \n",
"print(\"Termination Pairs for Second Interface (Material2, First Interface Substrate)\")\n",
"for idx, termination_pair in enumerate(termination_pairs_12):\n",
" print(f\" {idx}: {termination_pair}\")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "41b3d541c1ebfe5a",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 3.3. Select Termination Pair for Second Interface\n"
- ],
+ "id": "822c79480c3d7965",
"metadata": {
"collapsed": false
},
- "id": "822c79480c3d7965"
+ "source": [
+ "### 3.3. Select Termination Pair for Second Interface\n"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "f9d2b5429447338e",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
- "termination_pair_index_12 = TERMINATION_PAIR_INDEX_12\n",
+ "# Select terminations for Material 2 and the substrate using the newer approach\n",
+ "material2_termination = select_slab_termination(material2_slab_terminations, None) # None means use first termination\n",
+ "substrate_second_termination = substrate_second_slab_terminations[0] # Use the first (and only) termination\n",
+ "\n",
+ "# Create termination pair\n",
+ "termination_pair_second = (material2_termination, substrate_second_termination)\n",
"\n",
- "termination_pair_second = termination_pairs_12[termination_pair_index_12]\n",
+ "# Allow for interactive selection if enabled\n",
"if IS_TERMINATIONS_SELECTION_INTERACTIVE:\n",
+ " termination_pair_index_12 = TERMINATION_PAIR_INDEX_12\n",
+ " termination_pair_second = termination_pairs_12[termination_pair_index_12]\n",
" if sys.platform == \"emscripten\":\n",
" termination_pair_second = await ui_prompt_select_array_element_by_index_pyodide(\n",
" termination_pairs_12,\n",
@@ -570,163 +591,191 @@
" element_name=\"Material2/First Interface termination pair\"\n",
" )"
],
- "metadata": {
- "collapsed": false
- },
- "id": "f9d2b5429447338e",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 3.4. Initialize Interface Configuration for Second Interface\n"
- ],
+ "id": "796e3604d6bd4c60",
"metadata": {
"collapsed": false
},
- "id": "796e3604d6bd4c60"
+ "source": [
+ "### 3.4. Initialize Interface Configuration for Second Interface\n"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
- "source": [
- "from mat3ra.made.tools.build.interface import InterfaceConfiguration\n",
- "\n",
- "material2_termination, substrate_second_termination = termination_pair_second\n",
- "interface_configuration_12 = InterfaceConfiguration(\n",
- " film_configuration=material2_slab_configuration,\n",
- " substrate_configuration=substrate_second_slab_configuration,\n",
- " film_termination=material2_termination,\n",
- " substrate_termination=substrate_second_termination,\n",
- " distance=INTERFACE_12_DISTANCE,\n",
- " vacuum=FINAL_INTERFACE_VACUUM\n",
- ")"
- ],
+ "id": "fa7e6b937d2b78a0",
"metadata": {
"collapsed": false
},
- "id": "fa7e6b937d2b78a0",
+ "source": [
+ "# Create slab configurations and slabs for the second interface using the newer approach\n",
+ "material2_termination, substrate_second_termination = termination_pair_second\n",
+ "\n",
+ "# Slab configuration for Material 2 - using correct parameters like ZSL notebook\n",
+ "material2_slab_config = SlabConfiguration.from_parameters(\n",
+ " material_or_dict=material2,\n",
+ " miller_indices=MATERIAL_2_MILLER_INDICES,\n",
+ " number_of_layers=MATERIAL_2_THICKNESS,\n",
+ " vacuum=0.0, # Set vacuum to 0 for interface creation\n",
+ " termination_formula=None, # Will use selected termination\n",
+ " use_conventional_cell=True\n",
+ ")\n",
+ "\n",
+ "# Build the Material 2 slab\n",
+ "material2_slab = SlabBuilder().get_material(material2_slab_config)\n",
+ "\n",
+ "# For the substrate (first interface), we'll use it as-is since it's already built"
+ ],
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 3.5. Set Strain Matching Parameters and Generate Second Interface\n"
- ],
+ "id": "3816e1b290f7e5d0",
"metadata": {
"collapsed": false
},
- "id": "3816e1b290f7e5d0"
+ "source": [
+ "### 3.5. Set Strain Matching Parameters and Generate Second Interface\n"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "6f30c6961f7abbfe",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
- "zsl_strain_matching_parameters_12 = ZSLStrainMatchingParameters(\n",
- " max_area=MAX_AREA_12\n",
+ "# Set up ZSL Interface Analyzer for the second interface\n",
+ "# Note: For the second interface, we need to create a slab configuration for the substrate (first interface)\n",
+ "substrate_second_slab_config = SlabConfiguration.from_parameters(\n",
+ " material_or_dict=substrate_second,\n",
+ " miller_indices=(0, 0, 1), # Z-orientation for the first interface\n",
+ " number_of_layers=1, # One unit cell thick\n",
+ " vacuum=0.0,\n",
+ " termination_formula=None,\n",
+ " use_conventional_cell=True\n",
")\n",
"\n",
- "matched_interfaces_builder_12 = ZSLStrainMatchingInterfaceBuilder(\n",
- " build_parameters=ZSLStrainMatchingInterfaceBuilderParameters(\n",
- " strain_matching_parameters=zsl_strain_matching_parameters_12\n",
- " )\n",
+ "zsl_analyzer_12 = ZSLInterfaceAnalyzer(\n",
+ " substrate_slab_configuration=substrate_second_slab_config,\n",
+ " film_slab_configuration=material2_slab_config,\n",
+ " max_area=MAX_AREA_12,\n",
+ " max_area_ratio_tol=0.09, # Default tolerance\n",
+ " max_angle_tol=0.03, # Default tolerance\n",
+ " max_length_tol=0.03 # Default tolerance\n",
")\n",
"\n",
- "interfaces_12_sorted = matched_interfaces_builder_12.get_materials(configuration=interface_configuration_12)"
+ "# Get ZSL matches for the second interface\n",
+ "matches_12 = zsl_analyzer_12.zsl_match_holders"
],
- "metadata": {
- "collapsed": false
- },
- "id": "6f30c6961f7abbfe",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 3.6. Plot and Select Second Interface\n"
- ],
+ "id": "32ded9bdae6ef429",
"metadata": {
"collapsed": false
},
- "id": "32ded9bdae6ef429"
+ "source": [
+ "### 3.6. Plot and Select Second Interface\n"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
- "source": [
- "plot_strain_vs_atoms(interfaces_12_sorted, PLOT_SETTINGS)\n",
- "\n",
- "# Select the first interface with the lowest strain and smallest number of atoms\n",
- "interfaces_slice_range_12 = slice(0, 1)\n",
- "selected_interfaces_12 = interfaces_12_sorted[interfaces_slice_range_12]"
- ],
+ "id": "43f233403393eb2a",
"metadata": {
"collapsed": false
},
- "id": "43f233403393eb2a",
+ "source": [
+ "plot_strain_vs_area(matches_12, PLOT_SETTINGS)\n",
+ "\n",
+ "# Select the interface with the lowest strain and smallest number of atoms\n",
+ "selected_index_12 = 0\n",
+ "\n",
+ "# Create the second interface using the newer approach\n",
+ "interface_12 = create_zsl_interface_between_slabs(\n",
+ " substrate_slab=substrate_second,\n",
+ " film_slab=material2_slab,\n",
+ " gap=INTERFACE_12_DISTANCE,\n",
+ " vacuum=FINAL_INTERFACE_VACUUM,\n",
+ " match_id=selected_index_12,\n",
+ " max_area=MAX_AREA_12,\n",
+ ")\n",
+ "\n",
+ "selected_interfaces_12 = [interface_12]"
+ ],
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 3.7. Preview the Second Interface (Final Heterostructure)\n"
- ],
+ "id": "ed109941d5e29522",
"metadata": {
"collapsed": false
},
- "id": "ed109941d5e29522"
+ "source": [
+ "### 3.7. Preview the Second Interface (Final Heterostructure)\n"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "fffbf9243911a98",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"visualize(selected_interfaces_12, repetitions=[3, 3, 1])\n",
"visualize(selected_interfaces_12, repetitions=[3, 3, 1], rotation=\"-90x\")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "fffbf9243911a98",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "## 4. Preview the Final Heterostructure\n"
- ],
+ "id": "e98176e806c4aace",
"metadata": {
"collapsed": false
},
- "id": "e98176e806c4aace"
+ "source": [
+ "## 4. Preview the Final Heterostructure\n"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "47f9a1aa1578c37",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"visualize(selected_interfaces_12, repetitions=[3, 3, 1], title=\"Final Heterostructure (First Interface + Material2)\")\n",
"visualize(selected_interfaces_12, repetitions=[3, 3, 1], rotation=\"-90x\", title=\"Final Heterostructure (First Interface + Material2) Rotated\")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "47f9a1aa1578c37",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
+ "id": "946d5a41156bc1e1",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"## 5. Pass the Final Heterostructure to the Outside Runtime\n",
"\n",
"Pass the resulting heterostructure with an adjusted name to `set_materials()`.\n"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "946d5a41156bc1e1"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "1b466c32b0d82431",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"from utils.jupyterlite import set_materials\n",
"\n",
@@ -735,10 +784,7 @@
"\n",
"set_materials(final_heterostructure)"
],
- "metadata": {
- "collapsed": false
- },
- "id": "1b466c32b0d82431",
+ "outputs": [],
"execution_count": null
}
],
diff --git a/other/materials_designer/create_interface_with_min_strain_zsl.ipynb b/other/materials_designer/create_interface_with_min_strain_zsl.ipynb
index 205d91354..13f2f833b 100644
--- a/other/materials_designer/create_interface_with_min_strain_zsl.ipynb
+++ b/other/materials_designer/create_interface_with_min_strain_zsl.ipynb
@@ -45,39 +45,48 @@
}
},
{
+ "metadata": {},
"cell_type": "code",
"source": [
+ "from mat3ra.made.tools.build.slab.configurations import SlabConfiguration\n",
+ "\n",
"# Enable interactive selection of terminations via UI prompt\n",
- "IS_TERMINATIONS_SELECTION_INTERACTIVE = False \n",
+ "IS_TERMINATIONS_SELECTION_INTERACTIVE = False\n",
"\n",
- "FILM_INDEX = 1 # Index in the list of materials, to access as materials[FILM_INDEX]\n",
- "FILM_MILLER_INDICES = (0,0,1)\n",
+ "FILM_INDEX = 1 # Index in the list of materials, to access as materials[FILM_INDEX]\n",
+ "FILM_MILLER_INDICES = (0, 0, 1)\n",
"FILM_THICKNESS = 1 # in atomic layers\n",
+ "FILM_TERMINATION_FORMULA = None # if None, the first termination will be used\n",
"FILM_VACUUM = 0.0 # in angstroms\n",
"FILM_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n",
- "FILM_USE_ORTHOGONAL_Z = True\n",
+ "FILM_USE_ORTHOGONAL_C = True\n",
"\n",
"SUBSTRATE_INDEX = 0\n",
- "SUBSTRATE_MILLER_INDICES = (0,0,1)\n",
+ "SUBSTRATE_MILLER_INDICES = (0, 0, 1)\n",
"SUBSTRATE_THICKNESS = 3 # in atomic layers\n",
+ "SUBSTRATE_TERMINATION_FORMULA = None # if None, the first termination will be used\n",
"SUBSTRATE_VACUUM = 0.0 # in angstroms\n",
"SUBSTRATE_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n",
- "SUBSTRATE_USE_ORTHOGONAL_Z = True\n",
+ "SUBSTRATE_USE_ORTHOGONAL_C = True\n",
+ "\n",
+ "INTERFACE_DISTANCE = 3.0 # Gap between substrate and film, in Angstrom\n",
+ "INTERFACE_VACUUM = 10.0 # Vacuum over film, in Angstrom\n",
"\n",
- "# Maximum area for the superlattice search algorithm\n",
- "MAX_AREA = 50 # in Angstrom^2\n",
+ "# Whether to convert materials to conventional cells before creating slabs.\n",
+ "# To create interfaces with smaller cells, set this flag to False. (and pass already conventional cells as input)\n",
+ "USE_CONVENTIONAL_CELL = True\n",
+ "\n",
+ "# Maximum area for the superlattice search algorithm (the final interface area will be smaller)\n",
+ "MAX_AREA = 150 # in Angstrom^2\n",
"# Additional fine-tuning parameters (increase values to get more strained matches):\n",
- "MAX_AREA_TOLERANCE = 0.09 # in Angstrom^2\n",
- "MAX_ANGLE_TOLERANCE = 0.03\n",
- "MAX_LENGTH_TOLERANCE = 0.03\n",
- "# Set the termination pair indices\n",
- "TERMINATION_PAIR_INDEX = 0 # Will be overridden in interactive selection is used\n",
- "INTERFACE_DISTANCE = 3.0 # in Angstrom\n",
- "INTERFACE_VACUUM = 20.0 # in Angstrom"
+ "MAX_AREA_TOLERANCE = 0.09 # in Angstrom^2\n",
+ "MAX_LENGTH_TOLERANCE = 0.05\n",
+ "MAX_ANGLE_TOLERANCE = 0.02\n",
+ "\n",
+ "# Whether to reduce the resulting interface cell to the primitive cell after the interface creation.\n",
+ "# If the reduction causes unexpected results, try increasing the `MAX_AREA` for search.\n",
+ "REDUCE_RESULT_CELL_TO_PRIMITIVE = True"
],
- "metadata": {
- "collapsed": false
- },
"outputs": [],
"execution_count": null
},
@@ -98,10 +107,11 @@
"\n",
"if sys.platform == \"emscripten\":\n",
" import micropip\n",
- " \n",
+ "\n",
" await micropip.install('mat3ra-api-examples', deps=False)\n",
" await micropip.install('mat3ra-utils')\n",
" from mat3ra.utils.jupyterlite.packages import install_packages\n",
+ "\n",
" await install_packages(\"create_interface_with_min_strain_zsl.ipynb\")"
],
"metadata": {
@@ -125,7 +135,7 @@
"\n",
"materials = get_materials(globals())\n",
"substrate = materials[SUBSTRATE_INDEX]\n",
- "try: \n",
+ "try:\n",
" film = materials[FILM_INDEX]\n",
"except IndexError:\n",
" print(\"Film material not found. Re-using substrate material as film.\")\n",
@@ -150,6 +160,7 @@
"cell_type": "code",
"source": [
"from utils.visualize import visualize_materials as visualize\n",
+ "\n",
"visualize([substrate, film], repetitions=[3, 3, 1], rotation=\"0x\")"
],
"metadata": {
@@ -159,198 +170,143 @@
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
- "source": [
- "## 2. Configure slabs and select termination pair\n",
- "\n",
- "### 2.1. Create Substrate and Layer Slabs\n",
- "Slab Configuration lets define the slab thickness, vacuum, and the Miller indices of the interfacial plane and get the slabs with possible terminations.\n",
- "Define the substrate slab cell that will be used as a base for the interface and the film slab cell that will be placed on top of the substrate slab."
- ],
- "metadata": {}
+ "source": "## 2. Configure slabs for interface\n"
},
{
- "cell_type": "code",
- "source": [
- "from mat3ra.made.tools.build.slab import SlabConfiguration, get_terminations, create_slab\n",
- "\n",
- "film_slab_configuration = SlabConfiguration(\n",
- " bulk=film,\n",
- " miller_indices=FILM_MILLER_INDICES,\n",
- " number_of_layers=FILM_THICKNESS, # in atomic layers\n",
- " vacuum=FILM_VACUUM, # in angstroms\n",
- " xy_supercell_matrix=FILM_XY_SUPERCELL_MATRIX,\n",
- " use_orthogonal_z=FILM_USE_ORTHOGONAL_Z\n",
- ")\n",
- "\n",
- "substrate_slab_configuration = SlabConfiguration(\n",
- " bulk=substrate,\n",
- " miller_indices=SUBSTRATE_MILLER_INDICES,\n",
- " number_of_layers=SUBSTRATE_THICKNESS, # in atomic layers\n",
- " vacuum=SUBSTRATE_VACUUM, # in angstroms\n",
- " xy_supercell_matrix=SUBSTRATE_XY_SUPERCELL_MATRIX,\n",
- " use_orthogonal_z=SUBSTRATE_USE_ORTHOGONAL_Z\n",
- ")"
- ],
"metadata": {},
- "outputs": [],
- "execution_count": null
- },
- {
"cell_type": "markdown",
- "source": [
- "### 2.2. Get possible terminations for the slabs"
- ],
- "metadata": {
- "collapsed": false
- }
+ "source": "### 2.1. Get possible terminations for the slabs"
},
{
- "cell_type": "code",
- "source": [
- "film_slab_terminations = get_terminations(film_slab_configuration)\n",
- "substrate_slab_terminations = get_terminations(substrate_slab_configuration)"
- ],
"metadata": {
"collapsed": false
},
- "outputs": [],
- "execution_count": null
- },
- {
- "cell_type": "markdown",
- "source": [
- "### 2.3. Visualize slabs for all possible terminations"
- ],
- "metadata": {
- "collapsed": false
- }
- },
- {
"cell_type": "code",
"source": [
- "film_slabs = [create_slab(film_slab_configuration, termination) for termination in film_slab_terminations]\n",
- "substrate_slabs = [create_slab(substrate_slab_configuration, termination) for termination in substrate_slab_terminations]\n",
+ "from mat3ra.made.tools.build.slab.helpers import get_slab_terminations\n",
"\n",
- "visualize([{\"material\":slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in film_slabs ], repetitions=[3, 3, 1], rotation=\"-90x\")\n",
- "visualize([{\"material\":slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in substrate_slabs ], repetitions=[3, 3, 1], rotation=\"-90x\") "
+ "film_slab_terminations = get_slab_terminations(material=film, miller_indices=FILM_MILLER_INDICES)\n",
+ "substrate_slab_terminations = get_slab_terminations(material=substrate, miller_indices=SUBSTRATE_MILLER_INDICES)\n",
+ "print(\"Film slab terminations:\", film_slab_terminations)\n",
+ "print(\"Substrate slab terminations:\", substrate_slab_terminations)"
],
- "metadata": {
- "collapsed": false
- },
"outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
- "source": [
- "### 2.4. Print terminations for the interface"
- ],
- "metadata": {
- "collapsed": false
- }
+ "source": "### 2.2. Visualize slabs for all possible terminations"
},
{
+ "metadata": {
+ "collapsed": false
+ },
"cell_type": "code",
"source": [
- "from itertools import product\n",
+ "from mat3ra.made.tools.build.slab.helpers import create_slab\n",
+ "from mat3ra.made.tools.build.interface.helpers import create_zsl_interface_between_slabs\n",
+ "from mat3ra.made.tools.build.slab.termination_utils import select_slab_termination\n",
+ "\n",
+ "film_slabs = [create_slab(film, miller_indices=FILM_MILLER_INDICES, termination=termination, vacuum=0) for termination\n",
+ " in\n",
+ " film_slab_terminations]\n",
+ "\n",
+ "substrate_slabs = [create_slab(substrate, miller_indices=SUBSTRATE_MILLER_INDICES, termination=termination, vacuum=0)\n",
+ " for termination in\n",
+ " substrate_slab_terminations]\n",
"\n",
- "termination_pairs = list(product(film_slab_terminations, substrate_slab_terminations)) \n",
- "print(\"Termination Pairs (Film, Substrate)\")\n",
- "for idx, termination_pair in enumerate(termination_pairs):\n",
- " print(f\" {idx}: {termination_pair}\")"
+ "film_slabs_with_titles = [{\"material\": slab, \"title\": str(termination)} for slab, termination in\n",
+ " zip(film_slabs, film_slab_terminations)]\n",
+ "substrate_slabs_with_titles = [{\"material\": slab, \"title\": str(termination)} for slab, termination in\n",
+ " zip(substrate_slabs, substrate_slab_terminations)]\n",
+ "\n",
+ "visualize(film_slabs_with_titles, repetitions=[3, 3, 1], rotation=\"-90x\")\n",
+ "visualize(substrate_slabs_with_titles, repetitions=[3, 3, 1], rotation=\"-90x\")"
],
- "metadata": {
- "collapsed": false
- },
"outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
- "source": [
- "### 2.5. Select termination pair for the interface"
- ],
- "metadata": {
- "collapsed": false
- }
+ "source": "### 2.3. Select terminations for the Slabs"
},
{
+ "metadata": {},
"cell_type": "code",
"source": [
- "from utils.io import ui_prompt_select_array_element_by_index, ui_prompt_select_array_element_by_index_pyodide\n",
- "\n",
- "termination_pair_index = TERMINATION_PAIR_INDEX\n",
- "\n",
- "termination_pair = termination_pairs[termination_pair_index]\n",
- "if IS_TERMINATIONS_SELECTION_INTERACTIVE:\n",
- " if sys.platform == \"emscripten\":\n",
- " termination_pair = await ui_prompt_select_array_element_by_index_pyodide(termination_pairs, element_name=\"film/substrate termination pair\")\n",
- " else:\n",
- " termination_pair = ui_prompt_select_array_element_by_index(termination_pairs, element_name=\"film/substrate termination pair\")"
+ "film_termination = select_slab_termination(film_slab_terminations, FILM_TERMINATION_FORMULA)\n",
+ "substrate_termination = select_slab_termination(substrate_slab_terminations, SUBSTRATE_TERMINATION_FORMULA)"
],
- "metadata": {
- "collapsed": false
- },
"outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
"source": [
- "## 3. Create interfaces\n",
- "\n",
- "### 3.1. Initialize the Interface Configuration"
- ],
- "metadata": {
- "collapsed": false
- }
+ "### 2.4. Create Substrate and Layer Slabs\n",
+ "Slab Configuration lets define the slab thickness, vacuum, and the Miller indices of the interfacial plane and get the slabs with possible terminations.\n",
+ "Define the substrate slab cell that will be used as a base for the interface and the film slab cell that will be placed on top of the substrate slab."
+ ]
},
{
+ "metadata": {},
"cell_type": "code",
"source": [
- "from mat3ra.made.tools.build.interface import InterfaceConfiguration\n",
- "\n",
- "film_termination, substrate_termination = termination_pair\n",
- "interface_configuration = InterfaceConfiguration(\n",
- " film_configuration=film_slab_configuration,\n",
- " substrate_configuration=substrate_slab_configuration,\n",
- " film_termination=film_termination,\n",
- " substrate_termination=substrate_termination,\n",
- " distance_z=INTERFACE_DISTANCE,\n",
- " vacuum= INTERFACE_VACUUM\n",
- ")"
+ "from mat3ra.made.tools.build.slab.builders import SlabBuilder\n",
+ "\n",
+ "substrate_slab_config = SlabConfiguration.from_parameters(\n",
+ " material_or_dict=substrate,\n",
+ " miller_indices=SUBSTRATE_MILLER_INDICES,\n",
+ " number_of_layers=SUBSTRATE_THICKNESS,\n",
+ " vacuum=0.0,\n",
+ " termination_formula=SUBSTRATE_TERMINATION_FORMULA,\n",
+ " use_conventional_cell=USE_CONVENTIONAL_CELL\n",
+ ")\n",
+ "\n",
+ "film_slab_config = SlabConfiguration.from_parameters(\n",
+ " material_or_dict=film,\n",
+ " miller_indices=FILM_MILLER_INDICES,\n",
+ " number_of_layers=FILM_THICKNESS,\n",
+ " vacuum=0.0,\n",
+ " termination_formula=FILM_TERMINATION_FORMULA,\n",
+ " use_conventional_cell=USE_CONVENTIONAL_CELL\n",
+ ")\n",
+ "\n",
+ "substrate_slab = SlabBuilder().get_material(substrate_slab_config)\n",
+ "film_slab = SlabBuilder().get_material(film_slab_config)"
],
- "metadata": {
- "collapsed": false
- },
"outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
"source": [
- "### 3.2. Set Strain Matching Algorithm Parameters (Optional)\n",
+ "### 3.2. Analyze possible interfaces with ZSL Analyzer\n",
"The search algorithm for supercells matching can be tuned by setting its parameters directly, otherwise the default values are used."
- ],
- "metadata": {
- "collapsed": false
- }
+ ]
},
{
+ "metadata": {},
"cell_type": "code",
"source": [
- "from mat3ra.made.tools.build.interface import ZSLStrainMatchingParameters\n",
- "zsl_strain_matching_parameters = ZSLStrainMatchingParameters(\n",
+ "from mat3ra.made.tools.analyze.interface import ZSLInterfaceAnalyzer\n",
+ "\n",
+ "zsl_analyzer = ZSLInterfaceAnalyzer(\n",
+ " substrate_slab_configuration=substrate_slab_config,\n",
+ " film_slab_configuration=film_slab_config,\n",
" max_area=MAX_AREA,\n",
- " max_area_tol=MAX_AREA_TOLERANCE,\n",
- " max_angle_tol=MAX_ANGLE_TOLERANCE,\n",
+ " max_area_ratio_tol=MAX_AREA_TOLERANCE,\n",
" max_length_tol=MAX_LENGTH_TOLERANCE,\n",
+ " max_angle_tol=MAX_ANGLE_TOLERANCE,\n",
+ " reduce_result_cell=False # Reduces supercell matrices in analyzer\n",
")"
],
- "metadata": {
- "collapsed": false
- },
"outputs": [],
"execution_count": null
},
@@ -365,17 +321,9 @@
}
},
{
+ "metadata": {},
"cell_type": "code",
- "source": [
- "from mat3ra.made.tools.build.interface import ZSLStrainMatchingInterfaceBuilder, ZSLStrainMatchingInterfaceBuilderParameters\n",
- "\n",
- "matched_interfaces_builder = ZSLStrainMatchingInterfaceBuilder(build_parameters=ZSLStrainMatchingInterfaceBuilderParameters(strain_matching_parameters=zsl_strain_matching_parameters))\n",
- "\n",
- "interfaces_sorted_by_size_and_strain= matched_interfaces_builder.get_materials(configuration=interface_configuration)"
- ],
- "metadata": {
- "collapsed": false
- },
+ "source": "matches = zsl_analyzer.zsl_match_holders",
"outputs": [],
"execution_count": null
},
@@ -391,7 +339,7 @@
{
"cell_type": "code",
"source": [
- "from utils.plot import plot_strain_vs_atoms\n",
+ "from utils.plot import plot_strain_vs_area\n",
"\n",
"PLOT_SETTINGS = {\n",
" \"HEIGHT\": 600,\n",
@@ -399,7 +347,7 @@
" \"Y_SCALE\": \"log\", # or linear\n",
"}\n",
"\n",
- "plot_strain_vs_atoms(interfaces_sorted_by_size_and_strain, PLOT_SETTINGS)"
+ "plot_strain_vs_area(matches, PLOT_SETTINGS)"
],
"metadata": {
"collapsed": false
@@ -408,26 +356,52 @@
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
"source": [
"### 3.5. Select the interface\n",
"\n",
"Select the index for the interface with the lowest strain and the smallest number of atoms."
- ],
+ ]
+ },
+ {
"metadata": {
"collapsed": false
- }
+ },
+ "cell_type": "code",
+ "source": "selected_index = 0",
+ "outputs": [],
+ "execution_count": null
},
{
- "cell_type": "code",
+ "metadata": {},
+ "cell_type": "markdown",
"source": [
- "# select the first interface with the lowest strain and the smallest number of atoms\n",
- "interfaces_slice_range_or_index = slice(0, 1)\n",
- "selected_interfaces = interfaces_sorted_by_size_and_strain[interfaces_slice_range_or_index]"
- ],
+ "## 3. Create the interface\n",
+ "\n",
+ "### 3.1. Initialize the Interface Configuration"
+ ]
+ },
+ {
"metadata": {
"collapsed": false
},
+ "cell_type": "code",
+ "source": [
+ "\n",
+ "interface = create_zsl_interface_between_slabs(\n",
+ " substrate_slab=substrate_slab,\n",
+ " film_slab=film_slab,\n",
+ " gap=INTERFACE_DISTANCE,\n",
+ " vacuum=INTERFACE_VACUUM,\n",
+ " match_id=selected_index,\n",
+ " max_area=MAX_AREA,\n",
+ " max_area_ratio_tol=MAX_AREA_TOLERANCE,\n",
+ " max_length_tol=MAX_LENGTH_TOLERANCE,\n",
+ " max_angle_tol=MAX_ANGLE_TOLERANCE,\n",
+ " reduce_result_cell_to_primitive=REDUCE_RESULT_CELL_TO_PRIMITIVE,\n",
+ ")"
+ ],
"outputs": [],
"execution_count": null
},
@@ -443,8 +417,8 @@
{
"cell_type": "code",
"source": [
- "visualize(selected_interfaces, repetitions=[3, 3, 1])\n",
- "visualize(selected_interfaces, repetitions=[3, 3, 1], rotation=\"-90x\")"
+ "visualize(interface, repetitions=[1, 1, 1])\n",
+ "visualize(interface, repetitions=[1, 1, 1], rotation=\"-90x\")"
],
"metadata": {
"collapsed": false
@@ -464,7 +438,8 @@
"metadata": {},
"source": [
"from utils.jupyterlite import set_materials\n",
- "set_materials(selected_interfaces)"
+ "\n",
+ "set_materials(interface)"
],
"outputs": [],
"execution_count": null
diff --git a/other/materials_designer/create_interface_with_no_strain_matching.ipynb b/other/materials_designer/create_interface_with_no_strain_matching.ipynb
index 0dde92501..5fd58e1e7 100644
--- a/other/materials_designer/create_interface_with_no_strain_matching.ipynb
+++ b/other/materials_designer/create_interface_with_no_strain_matching.ipynb
@@ -37,13 +37,14 @@
}
},
{
+ "metadata": {},
"cell_type": "code",
- "outputs": [],
"source": [
"# Enable interactive selection of terminations via UI prompt\n",
"IS_TERMINATIONS_SELECTION_INTERACTIVE = False \n",
"# Enable scaling of the film slab atomic coordinates to match the substrate lattice (preserve coordinates in crystal units).\n",
"ENABLE_FILM_SCALING = True\n",
+ "\n",
"# Create slabs for the film and substrate when creating the interface, otherwise use provided materials directly.\n",
"CREATE_SLABS = True \n",
"\n",
@@ -51,24 +52,26 @@
"FILM_MILLER_INDICES = (0, 0, 1)\n",
"FILM_THICKNESS = 1 # in atomic layers\n",
"FILM_VACUUM = 0.0 # in angstroms\n",
+ "FILM_TERMINATION_FORMULA = None # if None, the first termination will be used\n",
"FILM_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n",
- "FILM_USE_ORTHOGONAL_Z = True\n",
+ "FILM_USE_ORTHOGONAL_C = True\n",
+ "FILM_XY_SHIFT = [0.0, 0.0] # in Angstroms, shift the film slab in the XY plane relative to the substrate slab\n",
"\n",
"SUBSTRATE_INDEX = 0\n",
"SUBSTRATE_MILLER_INDICES = (1, 1, 1)\n",
"SUBSTRATE_THICKNESS = 3 # in atomic layers\n",
"SUBSTRATE_VACUUM = 3.0 # in angstroms\n",
+ "SUBSTRATE_TERMINATION_FORMULA = None # if None, the first termination will be used\n",
"SUBSTRATE_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n",
- "SUBSTRATE_USE_ORTHOGONAL_Z = True\n",
+ "SUBSTRATE_USE_ORTHOGONAL_C = True\n",
+ "\n",
+ "# Whether to convert materials to conventional cells before creating slabs.\n",
+ "USE_CONVENTIONAL_CELL = False\n",
"\n",
- "# Set the termination pair indices\n",
- "TERMINATION_PAIR_INDEX = 0 # Will be overridden in interactive selection is used\n",
"INTERFACE_DISTANCE = 3.0 # in Angstrom\n",
"INTERFACE_VACUUM = 20.0 # in Angstrom"
],
- "metadata": {
- "collapsed": false
- },
+ "outputs": [],
"execution_count": null
},
{
@@ -84,7 +87,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"import sys\n",
"\n",
@@ -98,6 +100,7 @@
"metadata": {
"collapsed": false
},
+ "outputs": [],
"execution_count": null
},
{
@@ -112,7 +115,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
@@ -127,6 +129,7 @@
"metadata": {
"collapsed": false
},
+ "outputs": [],
"execution_count": null
},
{
@@ -140,7 +143,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"visualize([substrate, film], repetitions=[3, 3, 1], rotation=\"0x\")"
@@ -148,148 +150,124 @@
"metadata": {
"collapsed": false
},
+ "outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
"source": [
- "## 2. Configure slabs and select termination pair\n",
- "\n",
- "### 2.1. Create Substrate and Layer Slabs\n",
- "Slab Configuration lets define the slab thickness, vacuum, and the Miller indices of the interfacial plane and get the slabs with possible terminations.\n",
- "Define the substrate slab cell that will be used as a base for the interface and the film slab cell that will be placed on top of the substrate slab."
- ],
- "metadata": {
- "collapsed": false
- }
+ "## 2. Create slabs for the interface\n",
+ "\n"
+ ]
+ },
+ {
+ "metadata": {},
+ "cell_type": "markdown",
+ "source": "### 2.2. Get possible terminations for the slabs"
},
{
+ "metadata": {},
"cell_type": "code",
- "outputs": [],
"source": [
- "from mat3ra.made.tools.build.slab import SlabConfiguration, get_terminations, create_slab\n",
- "\n",
- "film_slab_configuration = SlabConfiguration(\n",
- " bulk=film,\n",
- " miller_indices=FILM_MILLER_INDICES,\n",
- " number_of_layers=FILM_THICKNESS, # in atomic layers\n",
- " vacuum=FILM_VACUUM, # in angstroms\n",
- " xy_supercell_matrix=FILM_XY_SUPERCELL_MATRIX,\n",
- " use_orthogonal_z=FILM_USE_ORTHOGONAL_Z\n",
- ")\n",
+ "from mat3ra.made.tools.build.slab.helpers import get_slab_terminations\n",
"\n",
- "substrate_slab_configuration = SlabConfiguration(\n",
- " bulk=substrate,\n",
- " miller_indices=SUBSTRATE_MILLER_INDICES,\n",
- " number_of_layers=SUBSTRATE_THICKNESS, # in atomic layers\n",
- " vacuum=SUBSTRATE_VACUUM, # in angstroms\n",
- " xy_supercell_matrix=SUBSTRATE_XY_SUPERCELL_MATRIX,\n",
- " use_orthogonal_z=SUBSTRATE_USE_ORTHOGONAL_Z\n",
- ")"
+ "film_slab_terminations = get_slab_terminations(film, miller_indices=FILM_MILLER_INDICES)\n",
+ "substrate_slab_terminations = get_slab_terminations(substrate, miller_indices=SUBSTRATE_MILLER_INDICES)"
],
- "metadata": {
- "collapsed": false
- },
+ "outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
- "source": [
- "### 2.2. Get possible terminations for the slabs"
- ],
- "metadata": {
- "collapsed": false
- }
+ "source": "### 2.3. Visualize slabs for all possible terminations"
},
{
- "cell_type": "code",
- "outputs": [],
- "source": [
- "film_slab_terminations = get_terminations(film_slab_configuration)\n",
- "substrate_slab_terminations = get_terminations(substrate_slab_configuration)"
- ],
"metadata": {
"collapsed": false
},
- "execution_count": null
- },
- {
- "cell_type": "markdown",
- "source": [
- "### 2.3. Visualize slabs for all possible terminations"
- ],
- "metadata": {
- "collapsed": false
- }
- },
- {
"cell_type": "code",
- "outputs": [],
"source": [
- "film_slabs = [create_slab(film_slab_configuration, termination) for termination in film_slab_terminations]\n",
- "substrate_slabs = [create_slab(substrate_slab_configuration, termination) for termination in substrate_slab_terminations]\n",
+ "from mat3ra.made.tools.build.slab.helpers import create_slab\n",
+ "from mat3ra.made.tools.build.slab.termination_utils import select_slab_termination\n",
"\n",
- "visualize([{\"material\":slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in film_slabs ], repetitions=[3, 3, 1], rotation=\"-90x\")\n",
- "visualize([{\"material\":slab, \"title\": slab.metadata[\"build\"][\"termination\"]} for slab in substrate_slabs ], repetitions=[3, 3, 1], rotation=\"-90x\") "
+ "film_slabs = [create_slab(film, miller_indices=FILM_MILLER_INDICES, termination=termination, vacuum=0) for termination\n",
+ " in\n",
+ " film_slab_terminations]\n",
+ "\n",
+ "substrate_slabs = [create_slab(substrate, miller_indices=SUBSTRATE_MILLER_INDICES, termination=termination, vacuum=0)\n",
+ " for termination in\n",
+ " substrate_slab_terminations]\n",
+ "\n",
+ "film_slabs_with_titles = [{\"material\": slab, \"title\": str(termination)} for slab, termination in\n",
+ " zip(film_slabs, film_slab_terminations)]\n",
+ "substrate_slabs_with_titles = [{\"material\": slab, \"title\": str(termination)} for slab, termination in\n",
+ " zip(substrate_slabs, substrate_slab_terminations)]\n",
+ "\n",
+ "visualize(film_slabs_with_titles, repetitions=[3, 3, 1], rotation=\"-90x\")\n",
+ "visualize(substrate_slabs_with_titles, repetitions=[3, 3, 1], rotation=\"-90x\")"
],
- "metadata": {
- "collapsed": false
- },
+ "outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
- "source": [
- "### 2.4. Print terminations for the interface"
- ],
- "metadata": {
- "collapsed": false
- }
+ "source": "### 2.3. Select terminations for the Slabs"
},
{
+ "metadata": {},
"cell_type": "code",
- "outputs": [],
"source": [
- "from itertools import product\n",
- "\n",
- "termination_pairs = list(product(film_slab_terminations, substrate_slab_terminations)) \n",
- "print(\"Termination Pairs (Film, Substrate)\")\n",
- "for idx, termination_pair in enumerate(termination_pairs):\n",
- " print(f\" {idx}: {termination_pair}\")\n",
- " "
+ "film_termination = select_slab_termination(film_slab_terminations, FILM_TERMINATION_FORMULA)\n",
+ "substrate_termination = select_slab_termination(substrate_slab_terminations, SUBSTRATE_TERMINATION_FORMULA)"
],
- "metadata": {
- "collapsed": false
- },
+ "outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
"source": [
- "### 2.5. Select termination pair for the interface"
- ],
- "metadata": {
- "collapsed": false
- }
+ "### 2.1. Create Substrate and Layer Slabs\n",
+ "Slab Configuration lets define the slab thickness, vacuum, and the Miller indices of the interfacial plane and get the slabs with possible terminations.\n",
+ "Define the substrate slab cell that will be used as a base for the interface and the film slab cell that will be placed on top of the substrate slab."
+ ]
},
{
+ "metadata": {},
"cell_type": "code",
- "outputs": [],
"source": [
- "from utils.io import ui_prompt_select_array_element_by_index, ui_prompt_select_array_element_by_index_pyodide\n",
+ "from mat3ra.made.tools.build.slab.helpers import create_slab\n",
"\n",
- "termination_pair_index = TERMINATION_PAIR_INDEX\n",
+ "if CREATE_SLABS:\n",
+ " film_slab = create_slab(\n",
+ " crystal=film,\n",
+ " miller_indices=FILM_MILLER_INDICES,\n",
+ " termination=film_termination,\n",
+ " number_of_layers=FILM_THICKNESS, # in atomic layers\n",
+ " vacuum=FILM_VACUUM, # in angstroms\n",
+ " xy_supercell_matrix=FILM_XY_SUPERCELL_MATRIX,\n",
+ " use_orthogonal_c=FILM_USE_ORTHOGONAL_C,\n",
+ " use_conventional_cell=USE_CONVENTIONAL_CELL\n",
+ " )\n",
"\n",
- "termination_pair = termination_pairs[termination_pair_index]\n",
- "if IS_TERMINATIONS_SELECTION_INTERACTIVE:\n",
- " if sys.platform == \"emscripten\":\n",
- " termination_pair = await ui_prompt_select_array_element_by_index_pyodide(termination_pairs, element_name=\"film/substrate termination pair\")\n",
- " else:\n",
- " termination_pair = ui_prompt_select_array_element_by_index(termination_pairs, element_name=\"film/substrate termination pair\")"
+ " substrate_slab = create_slab(\n",
+ " crystal=substrate,\n",
+ " miller_indices=SUBSTRATE_MILLER_INDICES,\n",
+ " termination=substrate_termination,\n",
+ " number_of_layers=SUBSTRATE_THICKNESS, # in atomic layers\n",
+ " vacuum=SUBSTRATE_VACUUM, # in angstroms\n",
+ " xy_supercell_matrix=SUBSTRATE_XY_SUPERCELL_MATRIX,\n",
+ " use_orthogonal_c=SUBSTRATE_USE_ORTHOGONAL_C,\n",
+ " use_conventional_cell=USE_CONVENTIONAL_CELL\n",
+ " )\n",
+ "else:\n",
+ " film_slab = film\n",
+ " substrate_slab = substrate\n"
],
- "metadata": {
- "collapsed": false
- },
+ "outputs": [],
"execution_count": null
},
{
@@ -297,71 +275,35 @@
"metadata": {},
"source": [
"## 3. Create an interface\n",
- "### 3.1. Initialize the Interface Configuration\n",
+ "### 3.1. Create an interface with no strain matching\n",
"We use no strain matching for the interface construction. Substrate slab cell is used as a base and the film slab is placed on top of it with the specified distance."
]
},
{
- "cell_type": "code",
- "execution_count": null,
"metadata": {},
- "outputs": [],
+ "cell_type": "code",
"source": [
- "from mat3ra.made.tools.build.interface import InterfaceConfiguration, create_interface\n",
+ "from mat3ra.made.tools.build.interface.helpers import create_simple_interface_between_slabs\n",
"\n",
- "film_termination, substrate_termination = termination_pair\n",
- "interface_configuration = InterfaceConfiguration(\n",
- " film_configuration=film_slab_configuration,\n",
- " substrate_configuration=substrate_slab_configuration,\n",
- " film_termination=film_termination,\n",
- " substrate_termination=substrate_termination,\n",
- " interface_distance=INTERFACE_DISTANCE, # in Angstrom\n",
- " interface_vacuum=INTERFACE_VACUUM # in Angstrom\n",
+ "interface = create_simple_interface_between_slabs(\n",
+ " film_slab=film_slab,\n",
+ " substrate_slab=substrate_slab,\n",
+ " gap =INTERFACE_DISTANCE,\n",
+ " vacuum=INTERFACE_VACUUM,\n",
+ " xy_shift=FILM_XY_SHIFT\n",
")"
- ]
- },
- {
- "cell_type": "markdown",
- "source": [
- "### 3.2. Scale the film slab to match the substrate lattice (optional)"
],
- "metadata": {
- "collapsed": false
- }
- },
- {
- "cell_type": "code",
"outputs": [],
- "source": [
- "from mat3ra.made.tools.build.interface import SimpleInterfaceBuilder, SimpleInterfaceBuilderParameters\n",
- "\n",
- "builder = SimpleInterfaceBuilder(build_parameters=SimpleInterfaceBuilderParameters(scale_film=ENABLE_FILM_SCALING, create_slabs=CREATE_SLABS))\n",
- "interface = builder.get_material(configuration=interface_configuration)"
- ],
- "metadata": {
- "collapsed": false
- },
"execution_count": null
},
{
- "cell_type": "markdown",
- "source": [
- "## 4. Preview the selected material"
- ],
- "metadata": {
- "collapsed": false
- }
- },
- {
+ "metadata": {},
"cell_type": "code",
- "outputs": [],
"source": [
"visualize([interface], repetitions=[3, 3, 1])\n",
"visualize([interface], repetitions=[3, 3, 1], rotation=\"-90x\")"
],
- "metadata": {
- "collapsed": false
- },
+ "outputs": [],
"execution_count": null
},
{
@@ -373,13 +315,13 @@
},
{
"cell_type": "code",
- "execution_count": null,
"metadata": {},
- "outputs": [],
"source": [
"from utils.jupyterlite import set_materials\n",
"set_materials(interface)"
- ]
+ ],
+ "outputs": [],
+ "execution_count": null
}
],
"metadata": {
diff --git a/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb b/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb
index a700eb7e6..9986ddcff 100644
--- a/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb
+++ b/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb
@@ -40,15 +40,15 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
- "MATERIAL_INDEX = 0 # Index of the material in the list of materials\n",
+ "MATERIAL_INDEX = 0 # Index of the material in the list of materials, should be an interface\n",
"# Maximum force tolerance for the relaxation to stop, in eV/Å\n",
"FMAX = 0.05"
],
"metadata": {
"collapsed": false
},
+ "outputs": [],
"execution_count": null
},
{
@@ -63,7 +63,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"import sys\n",
"\n",
@@ -77,6 +76,7 @@
"metadata": {
"collapsed": false
},
+ "outputs": [],
"execution_count": null
},
{
@@ -91,15 +91,15 @@
},
{
"cell_type": "code",
- "execution_count": null,
"metadata": {},
- "outputs": [],
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
"materials = get_materials(globals())\n",
"interface = materials[MATERIAL_INDEX]"
- ]
+ ],
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -112,13 +112,13 @@
},
{
"cell_type": "code",
- "execution_count": null,
"metadata": {},
- "outputs": [],
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"visualize(interface, repetitions=[3, 3, 1], rotation=\"0x\")"
- ]
+ ],
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -132,7 +132,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from ase.optimize import BFGS\n",
"from ase.calculators.emt import EMT\n",
@@ -147,6 +146,7 @@
"metadata": {
"collapsed": false
},
+ "outputs": [],
"execution_count": null
},
{
@@ -160,7 +160,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from mat3ra.utils.jupyterlite.plot import create_realtime_plot, create_update_callback\n",
"from mat3ra.made.tools.convert import from_ase\n",
@@ -197,11 +196,12 @@
"dyn.run(fmax=OPTIMIZATION_PARAMETERS[\"FMAX\"])\n",
"\n",
"ase_final_interface = ase_interface\n",
- "final_interface = Material(from_ase(ase_final_interface))"
+ "final_interface = Material.create(from_ase(ase_final_interface))"
],
"metadata": {
"collapsed": false
},
+ "outputs": [],
"execution_count": null
},
{
@@ -213,12 +213,12 @@
},
{
"cell_type": "code",
- "execution_count": null,
"metadata": {},
- "outputs": [],
"source": [
"visualize([{\"material\": interface, \"title\": \"original\"}, {\"material\":final_interface, \"title\":\"relaxed\"}], rotation= \"-90x\", repetitions=[3, 3, 1])\n"
- ]
+ ],
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -230,9 +230,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
"metadata": {},
- "outputs": [],
"source": [
"from mat3ra.made.tools.calculate import calculate_total_energy, calculate_interfacial_energy\n",
"\n",
@@ -244,7 +242,9 @@
"print(f\"Starting interface energy: {original_energy:.4f} eV\")\n",
"print(f\"Relaxed interface energy: {relaxed_energy:.4f} eV\")\n",
"print(f\"Interfacial energy: {interfacial_energy:.4f} eV\")"
- ]
+ ],
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -257,7 +257,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import set_materials\n",
"final_interface.name = f\"{interface.name}, Relaxed with EMT\" if \"Relaxed\" not in interface.name else interface.name\n",
@@ -266,6 +265,7 @@
"metadata": {
"collapsed": false
},
+ "outputs": [],
"execution_count": null
}
],
diff --git a/other/materials_designer/create_island_defect.ipynb b/other/materials_designer/create_island_defect.ipynb
index 2af826181..8d6ee4376 100644
--- a/other/materials_designer/create_island_defect.ipynb
+++ b/other/materials_designer/create_island_defect.ipynb
@@ -39,6 +39,7 @@
{
"cell_type": "code",
"source": [
+ "\n",
"# Shape-specific parameters\n",
"# Choose the island shape: 'cylinder', 'sphere', 'box', or 'triangular_prism'\n",
"# and the corresponding parameters\n",
@@ -52,7 +53,7 @@
"# Common parameters\n",
"CENTER_POSITION = [0.5, 0.5, 0.5] # Center of the island\n",
"USE_CARTESIAN_COORDINATES = False # Use Cartesian coordinates for the island\n",
- "NUMBER_OF_ADDED_LAYERS = 1 # Number of layers to add to the island\n",
+ "NUMBER_OF_ADDED_LAYERS = 3 # Number of layers to add to the island\n",
"\n",
"# Vacuum parameters for builder\n",
"AUTO_ADD_VACUUM = True # Automatically add vacuum to the slab\n",
@@ -63,7 +64,7 @@
" \"miller_indices\": (0,0,1),\n",
" \"thickness\": 3,\n",
" \"vacuum\": 5.0,\n",
- " \"use_orthogonal_z\": True,\n",
+ " \"use_orthogonal_c\": True,\n",
" \"xy_supercell_matrix\": [[3, 0], [0, 3]]\n",
"}\n",
"\n",
@@ -163,22 +164,22 @@
{
"cell_type": "code",
"source": [
- "from mat3ra.made.tools.build.slab import create_slab, SlabConfiguration\n",
+ "from mat3ra.made.tools.build.slab.helpers import create_slab\n",
"from utils.visualize import visualize_materials as visualize\n",
"\n",
"slab = materials[0]\n",
- "if not slab.metadata or slab.metadata[\"build\"][\"configuration\"][\"type\"] != SlabConfiguration.__name__:\n",
+ "\n",
+ "if not slab.metadata or not slab.metadata.build:\n",
" print(\"The material is not a slab. Creating a new slab...\")\n",
- " slab_config = SlabConfiguration(\n",
- " bulk=materials[0],\n",
+ " slab = create_slab(\n",
+ " crystal=slab,\n",
" miller_indices=DEFAULT_SLAB_PARAMETERS[\"miller_indices\"],\n",
" number_of_layers=DEFAULT_SLAB_PARAMETERS[\"thickness\"],\n",
" vacuum= DEFAULT_SLAB_PARAMETERS[\"vacuum\"],\n",
- " use_orthogonal_z=DEFAULT_SLAB_PARAMETERS[\"use_orthogonal_z\"],\n",
+ " use_orthogonal_c=DEFAULT_SLAB_PARAMETERS[\"use_orthogonal_c\"],\n",
" xy_supercell_matrix=DEFAULT_SLAB_PARAMETERS[\"xy_supercell_matrix\"]\n",
" )\n",
- " \n",
- " slab = create_slab(slab_config)\n",
+ "\n",
"\n",
"visualize([{\"material\": slab, \"title\": \"Original material\"}])\n",
"visualize([{\"material\": slab, \"title\": \"Original material\"}], rotation=\"-90x\")"
@@ -194,7 +195,7 @@
"cell_type": "markdown",
"source": [
"## 2. Create the Target Material\n",
- "### 2.1. Initialize the defect configuration and builder"
+ "### 2.1. Initialize the defect conditions"
],
"metadata": {
"collapsed": false
@@ -204,21 +205,12 @@
{
"cell_type": "code",
"source": [
- "from mat3ra.made.tools.build.defect import IslandSlabDefectConfiguration\n",
+ "from mat3ra.made.tools.utils.coordinate import CylinderCoordinateCondition\n",
"\n",
- "\n",
- "island_config = IslandSlabDefectConfiguration.from_dict(\n",
- " crystal=slab,\n",
- " condition=SHAPE_PARAMETERS,\n",
- " number_of_added_layers = NUMBER_OF_ADDED_LAYERS\n",
- ")\n",
- "\n",
- "from mat3ra.made.tools.build.defect import IslandSlabDefectBuilder, SlabDefectBuilderParameters\n",
- "params = SlabDefectBuilderParameters(\n",
- " auto_add_vacuum=AUTO_ADD_VACUUM,\n",
- " vacuum_thickness=VACUUM_THICKNESS,\n",
- ")\n",
- "builder = IslandSlabDefectBuilder(build_parameters=params)"
+ "condition = CylinderCoordinateCondition(\n",
+ " center_position=CENTER_POSITION,\n",
+ " radius=SHAPE_PARAMETERS['radius'],\n",
+ ")"
],
"metadata": {
"collapsed": false
@@ -240,7 +232,14 @@
{
"cell_type": "code",
"source": [
- "slab_with_island = builder.get_material(island_config)"
+ "from mat3ra.made.tools.build.defect.island.helpers import create_island_defect\n",
+ "\n",
+ "slab_with_island = create_island_defect(\n",
+ " slab=slab,\n",
+ " condition=condition,\n",
+ " use_cartesian_coordinates=USE_CARTESIAN_COORDINATES,\n",
+ " number_of_added_layers=NUMBER_OF_ADDED_LAYERS,\n",
+ ")\n"
],
"metadata": {
"collapsed": false
diff --git a/other/materials_designer/create_island_defect_custom.ipynb b/other/materials_designer/create_island_defect_custom.ipynb
index 5cb4f3e03..3328fbbcb 100644
--- a/other/materials_designer/create_island_defect_custom.ipynb
+++ b/other/materials_designer/create_island_defect_custom.ipynb
@@ -40,11 +40,11 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"import sys\n",
"from typing import List\n",
"\n",
+ "\n",
"if sys.platform == \"emscripten\":\n",
" import micropip\n",
" await micropip.install('mat3ra-api-examples', deps=False)\n",
@@ -56,6 +56,7 @@
"collapsed": false
},
"id": "b1216c665d6cf493",
+ "outputs": [],
"execution_count": null
},
{
@@ -69,15 +70,15 @@
"id": "c360bd0ea9a5f262"
},
{
+ "metadata": {},
"cell_type": "code",
- "outputs": [],
"source": [
"import numpy as np\n",
"from mat3ra.made.tools.utils.coordinate import CoordinateCondition\n",
"\n",
"# Custom Coordinate Condition for a torus shape\n",
"class CustomCoordinateCondition(CoordinateCondition):\n",
- " center: List[float] = [0.5, 0.5, 0.5]\n",
+ " center: List[float] = [0.5, 0.5, 0.0]\n",
" major_radius: float = 0.5\n",
" minor_radius: float = 0.1 \n",
"\n",
@@ -89,10 +90,8 @@
" distance_to_torus = np.sqrt((xy_distance - self.major_radius) ** 2 + (coord[2] - self.center[2]) ** 2)\n",
" return distance_to_torus <= self.minor_radius\n"
],
- "metadata": {
- "collapsed": false
- },
- "id": "9d8b1890b34d850a",
+ "id": "55f4289a6545c504",
+ "outputs": [],
"execution_count": null
},
{
@@ -106,31 +105,28 @@
"id": "535bbac2c3f2832b"
},
{
+ "metadata": {},
"cell_type": "code",
- "outputs": [],
"source": [
"CENTER_POSITION = [0.5, 0.5, 0.5] # Center of the torus in crystal coordinates\n",
"MAJOR_RADIUS = 0.3 # Major radius of the torus\n",
"MINOR_RADIUS = 0.1 # Minor radius of the torus\n",
+ "USE_CARTESIAN_COORDINATES = False # Use Cartesian coordinates for the condition\n",
"\n",
"NUMBER_OF_ADDED_LAYERS = 3 # Number of layers to add to the defect\n",
"\n",
- "AUTO_ADD_VACUUM = True # Automatically add vacuum to the slab\n",
- "VACUUM_THICKNESS = 5.0 # Thickness of the vacuum to add\n",
"\n",
"# Create slab with default parameters if imported material is not a slab\n",
"DEFAULT_SLAB_PARAMETERS = {\n",
" \"miller_indices\": (0,0,1),\n",
" \"thickness\": 3,\n",
" \"vacuum\": 5.0,\n",
- " \"use_orthogonal_z\": True,\n",
+ " \"use_orthogonal_c\": True,\n",
" \"xy_supercell_matrix\": [[10, 0], [0, 10]]\n",
"}"
],
- "metadata": {
- "collapsed": false
- },
- "id": "79924b8b23c8850b",
+ "id": "4f6c437b81325730",
+ "outputs": [],
"execution_count": null
},
{
@@ -145,7 +141,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"coordinate_condition = CustomCoordinateCondition(\n",
" center=CENTER_POSITION,\n",
@@ -157,6 +152,7 @@
"collapsed": false
},
"id": "87c3850f6c7178b2",
+ "outputs": [],
"execution_count": null
},
{
@@ -171,7 +167,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import get_materials\n",
"materials = get_materials(globals())"
@@ -180,6 +175,7 @@
"collapsed": false
},
"id": "be38fdda1984c654",
+ "outputs": [],
"execution_count": null
},
{
@@ -194,25 +190,22 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
- "from mat3ra.made.tools.build.slab import create_slab, SlabConfiguration\n",
+ "from mat3ra.made.tools.build.slab.helpers import create_slab\n",
"from utils.visualize import visualize_materials as visualize\n",
"\n",
"slab = materials[0]\n",
- "if not slab.metadata or slab.metadata[\"build\"][\"configuration\"][\"type\"] != SlabConfiguration.__name__:\n",
+ "if not slab.metadata or not slab.metadata.build:\n",
" print(\"The material is not a slab. Creating a new slab...\")\n",
- " slab_config = SlabConfiguration(\n",
- " bulk=materials[0],\n",
+ " slab = create_slab(\n",
+ " crystal=materials[0],\n",
" miller_indices=DEFAULT_SLAB_PARAMETERS[\"miller_indices\"],\n",
" number_of_layers=DEFAULT_SLAB_PARAMETERS[\"thickness\"],\n",
" vacuum= DEFAULT_SLAB_PARAMETERS[\"vacuum\"],\n",
- " use_orthogonal_z=DEFAULT_SLAB_PARAMETERS[\"use_orthogonal_z\"],\n",
+ " use_orthogonal_c=DEFAULT_SLAB_PARAMETERS[\"use_orthogonal_c\"],\n",
" xy_supercell_matrix=DEFAULT_SLAB_PARAMETERS[\"xy_supercell_matrix\"]\n",
" )\n",
" \n",
- " slab = create_slab(slab_config)\n",
- "\n",
"visualize([{\"material\": slab, \"title\": \"Original material\"}])\n",
"visualize([{\"material\": slab, \"title\": \"Original material\"}], rotation=\"-90x\")"
],
@@ -220,14 +213,12 @@
"collapsed": false
},
"id": "7fcb1e02e84c5f35",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "## 2. Create the Target Material\n",
- "### 2.1. Initialize the defect configuration and builder"
- ],
+ "source": "## 2. Create the Target Material",
"metadata": {
"collapsed": false
},
@@ -235,50 +226,21 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
- "from mat3ra.made.tools.build.defect import IslandSlabDefectConfiguration\n",
- "from mat3ra.made.tools.build.defect import IslandSlabDefectBuilder, SlabDefectBuilderParameters\n",
+ "from mat3ra.made.tools.build.defect.island.helpers import create_island_defect\n",
"\n",
- "island_config = IslandSlabDefectConfiguration(\n",
- " crystal=slab,\n",
+ "slab_with_island = create_island_defect(\n",
+ " slab=slab,\n",
" condition=coordinate_condition,\n",
- " number_of_added_layers=NUMBER_OF_ADDED_LAYERS\n",
- ")\n",
- "\n",
- "\n",
- "params = SlabDefectBuilderParameters(\n",
- " auto_add_vacuum=AUTO_ADD_VACUUM,\n",
- " vacuum_thickness=VACUUM_THICKNESS,\n",
- ")\n",
- "builder = IslandSlabDefectBuilder(build_parameters=params)"
+ " use_cartesian_coordinates=USE_CARTESIAN_COORDINATES,\n",
+ " number_of_added_layers=NUMBER_OF_ADDED_LAYERS,\n",
+ ")"
],
"metadata": {
"collapsed": false
},
"id": "e2d24109d3068c9e",
- "execution_count": null
- },
- {
- "cell_type": "markdown",
- "source": [
- "### 2.2. Create the island"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "489b51f0ee122c48"
- },
- {
- "cell_type": "code",
"outputs": [],
- "source": [
- "slab_with_island = builder.get_material(island_config)"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "a990fa35742d7269",
"execution_count": null
},
{
@@ -293,7 +255,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
" {\"material\": slab_with_island, \"title\": f\"Material with Island Defect\"}],\n",
@@ -306,6 +267,7 @@
"collapsed": false
},
"id": "509b18661a069e42",
+ "outputs": [],
"execution_count": null
},
{
@@ -320,7 +282,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import set_materials\n",
"\n",
@@ -330,6 +291,7 @@
"collapsed": false
},
"id": "61daa5afcbc078a9",
+ "outputs": [],
"execution_count": null
}
],
diff --git a/other/materials_designer/create_monolayer.ipynb b/other/materials_designer/create_monolayer.ipynb
index 4c4501e94..04bb3de53 100644
--- a/other/materials_designer/create_monolayer.ipynb
+++ b/other/materials_designer/create_monolayer.ipynb
@@ -32,7 +32,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"XY_SUPERCELL_MATRIX = [\n",
" [3, 0],\n",
@@ -45,6 +44,7 @@
"collapsed": false
},
"id": "a2c8922a4e627887",
+ "outputs": [],
"execution_count": null
},
{
@@ -60,7 +60,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"import sys\n",
"\n",
@@ -77,6 +76,7 @@
"collapsed": false
},
"id": "b0c332f1c1f451fd",
+ "outputs": [],
"execution_count": null
},
{
@@ -91,7 +91,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
@@ -102,6 +101,7 @@
"collapsed": false
},
"id": "74cd0d5a3881ab47",
+ "outputs": [],
"execution_count": null
},
{
@@ -116,7 +116,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"\n",
@@ -127,6 +126,7 @@
"collapsed": false
},
"id": "d6bea39864c23ab5",
+ "outputs": [],
"execution_count": null
},
{
@@ -141,86 +141,62 @@
},
{
"cell_type": "markdown",
- "source": [
- "### 2.1. Create slab configuration\n",
- "Slab Configuration lets define the slab thickness, vacuum, and the Miller indices of the interfacial plane and get the slabs with possible terminations.\n"
- ],
+ "source": "### 2.1. Create a monolayer unit cell",
"metadata": {
"collapsed": false
},
"id": "ee17958872d03410"
},
{
+ "metadata": {},
"cell_type": "code",
- "outputs": [],
"source": [
- "from mat3ra.made.tools.build.slab import SlabConfiguration\n",
+ "from mat3ra.made.tools.build.monolayer.helpers import create_monolayer\n",
"\n",
- "slab_configuration = number_of_layers=1,\n",
+ "monolayer = create_monolayer(\n",
+ " crystal=material,\n",
" vacuum=VACUUM,\n",
- " xy_supercell_matrix=XY_SUPERCELL_MATRIX,\n",
- " use_orthogonal_z=True,\n",
- " use_conventional_cell=True,\n",
")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "b8dc56881543c16c",
+ "id": "f05c4872edfef910",
+ "outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
- "source": [
- "### 2.2 Create the slab of Single Layer"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "661c76f9bab9f743"
+ "source": "### 2.2 Create a supercell",
+ "id": "372400a5610d7247"
},
{
+ "metadata": {},
"cell_type": "code",
- "outputs": [],
"source": [
- "from mat3ra.made.tools.modify import translate_to_z_level, filter_by_box\n",
- "from mat3ra.made.tools.build.slab import create_slab\n",
- "\n",
- "slab = create_slab(slab_configuration)\n",
+ "from mat3ra.made.tools.operations.core.unary import supercell\n",
"\n",
- "# Get only the top layer of two -- for AB stacked bilayers forming a 3D bulk basis\n",
- "if any(substring in material.name for substring in [\"3D\", \"Bulk\"]):\n",
- " centered_slab = translate_to_z_level(slab, z_level=\"center\")\n",
- " half_filtered_slab = filter_by_box(centered_slab, [0, 0, 0.5], [1, 1, 1])\n",
- " monolayer = translate_to_z_level(half_filtered_slab, z_level=\"center\")"
+ "monolayer = supercell(\n",
+ " material=monolayer,\n",
+ " supercell_matrix=XY_SUPERCELL_MATRIX, )"
],
- "metadata": {
- "collapsed": false
- },
- "id": "cf27e53c85adc447",
+ "id": "25d6681d5c1bfb0",
+ "outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
- "source": [
- "## 3. Visualize the result"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "527829d64a542d10"
+ "source": "## 3. Visualize the result",
+ "id": "82f9dfac4c711634"
},
{
+ "metadata": {},
"cell_type": "code",
- "outputs": [],
"source": [
"visualize(monolayer, repetitions=[1, 1, 1], rotation=\"0x\")\n",
"visualize(monolayer, repetitions=[1, 1, 1], rotation=\"-90x\")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "ee12ab13c210b953",
+ "id": "ab5c2f5ee249525c",
+ "outputs": [],
"execution_count": null
},
{
@@ -235,7 +211,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import set_materials\n",
"\n",
@@ -245,6 +220,7 @@
"collapsed": false
},
"id": "865c71d008d87beb",
+ "outputs": [],
"execution_count": null
}
],
diff --git a/other/materials_designer/create_nanoribbon.ipynb b/other/materials_designer/create_nanoribbon.ipynb
index 2be2be5ce..9a77e5a0f 100644
--- a/other/materials_designer/create_nanoribbon.ipynb
+++ b/other/materials_designer/create_nanoribbon.ipynb
@@ -41,19 +41,19 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"# Widths and lengths are in number of unit cells\n",
- "WIDTH = 3\n",
- "VACUUM_WIDTH = 2\n",
- "LENGTH = 10\n",
- "VACUUM_LENGTH = 0\n",
+ "WIDTH = 4 # in unit cells\n",
+ "LENGTH = 10 # in unit cells\n",
+ "VACUUM_WIDTH = 10.0 # in Angstroms\n",
+ "VACUUM_LENGTH = 10.0 # in Angstroms\n",
"EDGE_TYPE = \"zigzag\" # \"zigzag\" or \"armchair\""
],
"metadata": {
"collapsed": false
},
"id": "a40d7b697c413113",
+ "outputs": [],
"execution_count": null
},
{
@@ -69,7 +69,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"import sys\n",
"\n",
@@ -84,6 +83,7 @@
"collapsed": false
},
"id": "c6d9f8e57bef2f91",
+ "outputs": [],
"execution_count": null
},
{
@@ -99,7 +99,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import get_materials\n",
"materials = get_materials(globals())"
@@ -108,6 +107,7 @@
"collapsed": false
},
"id": "e0c53233ce728cc1",
+ "outputs": [],
"execution_count": null
},
{
@@ -122,25 +122,22 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"\n",
- "material = materials[0]\n",
+ "material = materials[1]\n",
"visualize(material, repetitions=[3, 3, 1], rotation=\"0x\")"
],
"metadata": {
"collapsed": false
},
"id": "897ba7aa4e402d24",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "## 2. Create the Nanoribbon\n",
- "### 2.1. Set nanoribbon parameters"
- ],
+ "source": "## 2. Create the Nanoribbon\n",
"metadata": {
"collapsed": false
},
@@ -148,48 +145,26 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
- "from mat3ra.made.tools.build.nanoribbon import NanoribbonBuilder, NanoribbonConfiguration\n",
+ "from mat3ra.made.tools.build.lattice_lines import EdgeTypes\n",
+ "from mat3ra.made.tools.build.nanoribbon.helpers import create_nanoribbon\n",
+ "\n",
"\n",
- "nanoribbon_configuration = NanoribbonConfiguration(\n",
+ "nanoribbon = create_nanoribbon(\n",
" material=material,\n",
" width=WIDTH,\n",
- " vacuum_width=VACUUM_WIDTH,\n",
" length=LENGTH,\n",
+ " vacuum_width=VACUUM_WIDTH,\n",
" vacuum_length=VACUUM_LENGTH,\n",
- " edge_type=EDGE_TYPE\n",
- ")\n",
- "\n",
- "\n",
- "builder = NanoribbonBuilder()"
+ " use_rectangular_lattice=True,\n",
+ " edge_type=EdgeTypes.zigzag if EDGE_TYPE == \"zigzag\" else EdgeTypes.armchair\n",
+ ")"
],
"metadata": {
"collapsed": false
},
"id": "1991efeeebe39db4",
- "execution_count": null
- },
- {
- "cell_type": "markdown",
- "source": [
- "### 2.2. Create the Nanoribbon"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "d296d7287618dc0b"
- },
- {
- "cell_type": "code",
"outputs": [],
- "source": [
- "nanoribbon = builder.get_material(nanoribbon_configuration)"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "302f417828a8fc9c",
"execution_count": null
},
{
@@ -204,7 +179,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"visualize([{\"material\": nanoribbon, \"title\": \"Nanoribbon\"}])"
@@ -213,6 +187,7 @@
"collapsed": false
},
"id": "1ee393a7f2ec3bc8",
+ "outputs": [],
"execution_count": null
},
{
@@ -227,7 +202,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import set_materials\n",
"set_materials(nanoribbon)"
@@ -236,6 +210,7 @@
"collapsed": false
},
"id": "29dfa0a329cca2fa",
+ "outputs": [],
"execution_count": null
}
],
diff --git a/other/materials_designer/create_nanowire.ipynb b/other/materials_designer/create_nanowire.ipynb
index 0fa734e4e..454a75333 100644
--- a/other/materials_designer/create_nanowire.ipynb
+++ b/other/materials_designer/create_nanowire.ipynb
@@ -32,7 +32,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"MILLER_INDICES= (0,0,1) # Miller indices of the nanowire direction\n",
"RADIUS = 5.0 # Wire radius in Angstroms\n",
@@ -44,6 +43,7 @@
"collapsed": false
},
"id": "2269749714d81b93",
+ "outputs": [],
"execution_count": null
},
{
@@ -59,7 +59,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"import sys\n",
"\n",
@@ -75,6 +74,7 @@
"collapsed": false
},
"id": "6dac92b719d539ec",
+ "outputs": [],
"execution_count": null
},
{
@@ -89,7 +89,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
@@ -100,6 +99,7 @@
"collapsed": false
},
"id": "b95701d7a0e593fe",
+ "outputs": [],
"execution_count": null
},
{
@@ -114,7 +114,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"visualize(material, repetitions=[3,3,3], rotation=\"0x\")\n",
@@ -124,6 +123,7 @@
"collapsed": false
},
"id": "c98ec170f3ee6d24",
+ "outputs": [],
"execution_count": null
},
{
@@ -139,22 +139,20 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"import math\n",
"from mat3ra.made.tools.build.supercell import create_supercell\n",
"from mat3ra.made.tools.modify import filter_by_cylinder, add_vacuum_sides\n",
- "from mat3ra.made.tools.build.slab import create_slab, SlabConfiguration\n",
+ "from mat3ra.made.tools.build.slab.helpers import create_slab\n",
"\n",
- "slab_config = SlabConfiguration(\n",
- " bulk=material,\n",
+ "slab_unit_cell = create_slab(\n",
+ " crystal=material,\n",
" miller_indices=MILLER_INDICES,\n",
" number_of_layers=1,\n",
" vacuum=0,\n",
- " use_orthogonal_z=True,\n",
+ " use_orthogonal_c=True,\n",
")\n",
"\n",
- "slab_unit_cell = create_slab(slab_config)\n",
"n_for_x = math.ceil(int(2*RADIUS / slab_unit_cell.lattice.a)) + 1\n",
"n_for_y = math.ceil(int(2*RADIUS / slab_unit_cell.lattice.b)) + 1\n",
"n_for_z = int(LENGTH / slab_unit_cell.lattice.c)\n",
@@ -166,6 +164,7 @@
"collapsed": false
},
"id": "c4b34b3287960dcc",
+ "outputs": [],
"execution_count": null
},
{
@@ -180,7 +179,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"rotate_90_degree_matrix = [[0, 0, 1], [0, 1, 0], [-1, 0, 0]]\n",
"nanowire_x = create_supercell(nanowire_z, supercell_matrix=rotate_90_degree_matrix)\n",
@@ -190,6 +188,7 @@
"collapsed": false
},
"id": "7401ab24726bf4e5",
+ "outputs": [],
"execution_count": null
},
{
@@ -204,7 +203,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"visualize(nanowire, repetitions=[1, 1, 1], rotation=\"0x\")\n",
"visualize(nanowire, repetitions=[1, 1, 1], rotation=\"-90x\")\n",
@@ -214,6 +212,7 @@
"collapsed": false
},
"id": "aea078560283ca95",
+ "outputs": [],
"execution_count": null
},
{
@@ -228,7 +227,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import set_materials\n",
"set_materials(nanowire)"
@@ -237,6 +235,7 @@
"collapsed": false
},
"id": "cdaf612bc6198546",
+ "outputs": [],
"execution_count": null
}
],
diff --git a/other/materials_designer/create_nanowire_custom_shape.ipynb b/other/materials_designer/create_nanowire_custom_shape.ipynb
index e70cd96de..ecd60a26b 100644
--- a/other/materials_designer/create_nanowire_custom_shape.ipynb
+++ b/other/materials_designer/create_nanowire_custom_shape.ipynb
@@ -42,7 +42,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"import sys\n",
"\n",
@@ -58,6 +57,7 @@
"collapsed": false
},
"id": "bd0fdddfd8880b40",
+ "outputs": [],
"execution_count": null
},
{
@@ -72,7 +72,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from typing import List\n",
"\n",
@@ -110,6 +109,7 @@
"collapsed": false
},
"id": "e93f72e7c37dea10",
+ "outputs": [],
"execution_count": null
},
{
@@ -124,7 +124,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
@@ -135,6 +134,7 @@
"collapsed": false
},
"id": "4b72580121ca40d0",
+ "outputs": [],
"execution_count": null
},
{
@@ -149,7 +149,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"visualize(material, repetitions=[3,3,3], rotation=\"0x\")\n",
@@ -159,6 +158,7 @@
"collapsed": false
},
"id": "d3cba46f185c1a1b",
+ "outputs": [],
"execution_count": null
},
{
@@ -174,21 +174,19 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from mat3ra.made.tools.build.supercell import create_supercell\n",
"from mat3ra.made.tools.modify import add_vacuum_sides, filter_by_condition_on_coordinates\n",
- "from mat3ra.made.tools.build.slab import create_slab, SlabConfiguration\n",
+ "from mat3ra.made.tools.build.slab.helpers import create_slab\n",
"\n",
- "slab_config = SlabConfiguration(\n",
- " bulk=material,\n",
+ "slab_unit_cell = create_slab(\n",
+ " crystal=material,\n",
" miller_indices=MILLER_INDICES,\n",
" number_of_layers=1,\n",
" vacuum=0,\n",
- " use_orthogonal_z=True,\n",
+ " use_orthogonal_c=True,\n",
")\n",
"\n",
- "slab_unit_cell = create_slab(slab_config)\n",
"supercell = create_supercell(slab_unit_cell, supercell_matrix=SUPERCELL_MATRIX)\n",
"nanowire_z = filter_by_condition_on_coordinates(supercell, condition=condition, use_cartesian_coordinates=USE_CARTESIAN_COORDINATES)\n",
"nanowire_z = add_vacuum_sides(nanowire_z, vacuum=VACUUM, on_x=True, on_y=True) "
@@ -197,6 +195,7 @@
"collapsed": false
},
"id": "2795d5bdbbaafbe6",
+ "outputs": [],
"execution_count": null
},
{
@@ -211,7 +210,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"rotate_90_degree_matrix = [[0, 0, 1], [0, 1, 0], [-1, 0, 0]]\n",
"nanowire_x = create_supercell(nanowire_z, supercell_matrix=rotate_90_degree_matrix)\n",
@@ -221,6 +219,7 @@
"collapsed": false
},
"id": "87534e47ecdb9dc6",
+ "outputs": [],
"execution_count": null
},
{
@@ -235,7 +234,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"visualize(nanowire, repetitions=[1, 1, 1], rotation=\"0x\")\n",
"visualize(nanowire, repetitions=[1, 1, 1], rotation=\"-90x\")\n",
@@ -245,6 +243,7 @@
"collapsed": false
},
"id": "aea078560283ca95",
+ "outputs": [],
"execution_count": null
},
{
@@ -259,7 +258,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import set_materials\n",
"set_materials(nanowire)"
@@ -268,6 +266,7 @@
"collapsed": false
},
"id": "cdaf612bc6198546",
+ "outputs": [],
"execution_count": null
}
],
diff --git a/other/materials_designer/create_perturbation.ipynb b/other/materials_designer/create_perturbation.ipynb
index a3e28ecdf..309be3e24 100644
--- a/other/materials_designer/create_perturbation.ipynb
+++ b/other/materials_designer/create_perturbation.ipynb
@@ -37,13 +37,10 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
- "# Sine wave perturbation parameters\n",
- "AMPLITUDE = 0.5\n",
- "WAVELENGTH = 1.0\n",
- "PHASE = 0.0\n",
- "AXIS = \"y\"\n",
+ "# string representation of the perturbation function, function of x, y, z variables\n",
+ "\n",
+ "perturbation_function = \"0.5 * sin (2 * pi * x) \"\n",
"\n",
"USE_CARTESIAN_COORDINATES = False\n",
"\n",
@@ -55,6 +52,7 @@
"collapsed": false
},
"id": "a40d7b697c413113",
+ "outputs": [],
"execution_count": null
},
{
@@ -70,7 +68,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"import sys\n",
"\n",
@@ -87,6 +84,7 @@
"collapsed": false
},
"id": "c6d9f8e57bef2f91",
+ "outputs": [],
"execution_count": null
},
{
@@ -102,7 +100,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
@@ -112,6 +109,7 @@
"collapsed": false
},
"id": "e0c53233ce728cc1",
+ "outputs": [],
"execution_count": null
},
{
@@ -126,7 +124,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"from mat3ra.made.tools.build.supercell import create_supercell\n",
@@ -139,6 +136,7 @@
"collapsed": false
},
"id": "897ba7aa4e402d24",
+ "outputs": [],
"execution_count": null
},
{
@@ -155,55 +153,21 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
- "from mat3ra.made.tools.build.perturbation import PerturbationConfiguration, SlabPerturbationBuilder, CellMatchingDistancePreservingSlabPerturbationBuilder\n",
- "from mat3ra.made.tools.utils.perturbation import SineWavePerturbationFunctionHolder\n",
- "\n",
- "perturbation_function = SineWavePerturbationFunctionHolder(\n",
- " amplitude=AMPLITUDE,\n",
- " wavelength=WAVELENGTH,\n",
- " phase=PHASE,\n",
- " axis=AXIS)\n",
+ "from mat3ra.made.tools.build.perturbation.helpers import create_perturbation\n",
"\n",
- "configuration = PerturbationConfiguration(\n",
+ "material_with_perturbation = create_perturbation(\n",
" material=supercell,\n",
- " perturbation_function_holder=perturbation_function,\n",
- " use_cartesian_coordinates=USE_CARTESIAN_COORDINATES)\n",
- "\n",
- "if PRESERVE_GEODESIC_DISTANCE:\n",
- " builder = CellMatchingDistancePreservingSlabPerturbationBuilder()\n",
- "else:\n",
- " builder = SlabPerturbationBuilder()"
+ " perturbation_function=perturbation_function,\n",
+ " is_isometric=PRESERVE_GEODESIC_DISTANCE,\n",
+ " use_cartesian_coordinates=USE_CARTESIAN_COORDINATES\n",
+ ")\n"
],
"metadata": {
"collapsed": false
},
"id": "1991efeeebe39db4",
- "execution_count": null
- },
- {
- "cell_type": "markdown",
- "source": [
- "### 2.2. Apply perturbation to the material"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "d296d7287618dc0b"
- },
- {
- "cell_type": "code",
"outputs": [],
- "source": [
- "from mat3ra.made.tools.build.perturbation import create_perturbation\n",
- "\n",
- "material_with_perturbation = create_perturbation(configuration, builder)"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "d77821f7d0b8c330",
"execution_count": null
},
{
@@ -218,7 +182,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"\n",
@@ -231,6 +194,7 @@
"collapsed": false
},
"id": "1ee393a7f2ec3bc8",
+ "outputs": [],
"execution_count": null
},
{
@@ -245,7 +209,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import set_materials\n",
"\n",
@@ -255,6 +218,7 @@
"collapsed": false
},
"id": "29dfa0a329cca2fa",
+ "outputs": [],
"execution_count": null
}
],
diff --git a/other/materials_designer/create_perturbation_custom.ipynb b/other/materials_designer/create_perturbation_custom.ipynb
index 4d68aa538..460473dda 100644
--- a/other/materials_designer/create_perturbation_custom.ipynb
+++ b/other/materials_designer/create_perturbation_custom.ipynb
@@ -48,7 +48,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"import sys\n",
"\n",
@@ -65,6 +64,7 @@
"collapsed": false
},
"id": "7a6e28cfae1a7b46",
+ "outputs": [],
"execution_count": null
},
{
@@ -79,7 +79,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"# Set whether to preserve geodesic distance and scale the cell accordingly to match PBC\n",
"PRESERVE_GEODESIC_DISTANCE = True\n",
@@ -94,6 +93,7 @@
"collapsed": false
},
"id": "a40d7b697c413113",
+ "outputs": [],
"execution_count": null
},
{
@@ -109,7 +109,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"import sympy as sp\n",
"\n",
@@ -130,6 +129,7 @@
"collapsed": false
},
"id": "203911c2413c7447",
+ "outputs": [],
"execution_count": null
},
{
@@ -145,7 +145,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
@@ -155,6 +154,7 @@
"collapsed": false
},
"id": "e0c53233ce728cc1",
+ "outputs": [],
"execution_count": null
},
{
@@ -169,7 +169,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"from mat3ra.made.tools.build.supercell import create_supercell\n",
@@ -182,6 +181,7 @@
"collapsed": false
},
"id": "897ba7aa4e402d24",
+ "outputs": [],
"execution_count": null
},
{
@@ -197,52 +197,22 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
- "from mat3ra.made.tools.build.perturbation import CellMatchingDistancePreservingSlabPerturbationBuilder, \\\n",
- " PerturbationConfiguration, SlabPerturbationBuilder\n",
- "from mat3ra.made.tools.utils.perturbation import PerturbationFunctionHolder\n",
+ "from mat3ra.made.tools.build.perturbation.helpers import create_perturbation\n",
"\n",
- "custom_perturbation_function = PerturbationFunctionHolder(function=custom_sympy_function,\n",
- " variables=variable_names)\n",
- "configuration_custom = PerturbationConfiguration(\n",
- " material=supercell,\n",
- " perturbation_function_holder=custom_perturbation_function,\n",
- " use_cartesian_coordinates=USE_CARTESIAN_COORDINATES)\n",
"\n",
- "if PRESERVE_GEODESIC_DISTANCE:\n",
- " builder = CellMatchingDistancePreservingSlabPerturbationBuilder()\n",
- "else:\n",
- " builder = SlabPerturbationBuilder()"
+ "material_with_perturbation = create_perturbation(\n",
+ " material=supercell,\n",
+ " perturbation_function=custom_sympy_function,\n",
+ " is_isometric=PRESERVE_GEODESIC_DISTANCE,\n",
+ " use_cartesian_coordinates=USE_CARTESIAN_COORDINATES\n",
+ ")\n"
],
"metadata": {
"collapsed": false
},
"id": "8d90932312c418ee",
- "execution_count": null
- },
- {
- "cell_type": "markdown",
- "source": [
- "### 2.2. Apply perturbation to the material"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "7695d5d1df6be2e3"
- },
- {
- "cell_type": "code",
"outputs": [],
- "source": [
- "from mat3ra.made.tools.build.perturbation import create_perturbation\n",
- "\n",
- "material_with_custom_perturbation = create_perturbation(configuration_custom, builder)"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "69ccc90b8c5c1191",
"execution_count": null
},
{
@@ -257,17 +227,17 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"visualize([\n",
- " {\"material\": material_with_custom_perturbation, \"title\": f\"Material with custom perturbation\"},\n",
- " {\"material\": material_with_custom_perturbation, \"title\": f\"Material with custom perturbation\", \"rotation\": \"-90x\"}\n",
+ " {\"material\": material_with_perturbation, \"title\": f\"Material with custom perturbation\"},\n",
+ " {\"material\": material_with_perturbation, \"title\": f\"Material with custom perturbation\", \"rotation\": \"-90x\"}\n",
"])"
],
"metadata": {
"collapsed": false
},
"id": "cbfe0878a16f6c83",
+ "outputs": [],
"execution_count": null
},
{
@@ -282,16 +252,16 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import set_materials\n",
"\n",
- "set_materials(material_with_custom_perturbation)"
+ "set_materials(material_with_perturbation)"
],
"metadata": {
"collapsed": false
},
"id": "29dfa0a329cca2fa",
+ "outputs": [],
"execution_count": null
}
],
diff --git a/other/materials_designer/create_point_defect.ipynb b/other/materials_designer/create_point_defect.ipynb
index f09fa057b..92d465612 100644
--- a/other/materials_designer/create_point_defect.ipynb
+++ b/other/materials_designer/create_point_defect.ipynb
@@ -2,8 +2,12 @@
"cells": [
{
"cell_type": "markdown",
+ "id": "f2e1e795020d7b3f",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
- "# Create point defects in a bulk material\n",
+ "# Create Multiple Point Defects in a Bulk Material\n",
"\n",
"Create a vacancy, add substitution or interstitial atom to provided Material.\n",
"\n",
@@ -18,72 +22,72 @@
"\n",
"1. For more information, see [Introduction](Introduction.ipynb)\n",
"\n"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "f2e1e795020d7b3f"
+ ]
},
{
"cell_type": "markdown",
+ "id": "5e43ff288847b784",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"## 1. Prepare the Environment\n",
"### 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
- },
- "id": "5e43ff288847b784"
+ ]
},
{
"cell_type": "code",
+ "id": "9d8b1890b34d850a",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"# Selected material will be used as a unit cell to create a supercell first.\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\": \"substitution\", # (e.g. \"vacancy\", \"substitution\", \"interstitial\")\n",
- " \"chemical_element\": \"C\", # Substitution element\n",
- " \"approximate_coordinate\": [0.0, 0.0, 0.0], # Approx. coord that will be resolved to the closest site\n",
- " \"use_cartesian_coordinates\": True, # Use cartesian or crystal coordinates\n",
+ " \"type\": \"substitution\",\n",
+ " \"coordinate\": [0.0, 0.0, 0.0], # Crystal coordinates\n",
+ " \"element\": \"C\",\n",
+ " \"placement_method\": \"closest_site\",\n",
+ " },\n",
+ " \n",
+ " {\n",
+ " \"type\": \"vacancy\",\n",
+ " \"coordinate\": [0.25, 0.25, 0.25], # Crystal coordinates \n",
+ " \"placement_method\": \"closest_site\",\n",
+ " },\n",
+ " \n",
+ " {\n",
+ " \"type\": \"interstitial\",\n",
+ " \"coordinate\": [0.75, 0.75, 0.75], # Crystal coordinates\n",
+ " \"element\": \"N\",\n",
+ " \"placement_method\": \"voronoi_site\",\n",
" },\n",
- "\n",
- " # Uncomment the next lines to create more defects\n",
- " # {\n",
- " # \"defect_type\": \"vacancy\", # Remove an atom at a specific site\n",
- " # \"site_id\": 0, # Index of the atom in the host material\n",
- " # },\n",
- " # {\n",
- " # \"defect_type\": \"interstitial\", # Add an atom at an interstitial site\n",
- " # \"coordinate\": [0.25, 0.25, 0.25], # Exact position\n",
- " # \"use_cartesian_coordinates\": False, # Use cartesian or crystal coordinates\n",
- " # \"chemical_element\": \"N\", # Add interstitial atom\n",
- " # }\n",
"]"
],
- "metadata": {
- "collapsed": false
- },
- "id": "9d8b1890b34d850a",
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 1.2. Install Packages\n",
- "The step executes only in Pyodide environment. For other environments, the packages should be installed via `pip install` (see [README](../../README.ipynb))."
- ],
+ "id": "bb64de5ff32649f8",
"metadata": {
"collapsed": false
},
- "id": "bb64de5ff32649f8"
+ "source": [
+ "### 1.2. Install Packages\n",
+ "The step executes only in Pyodide environment. For other environments, the packages should be installed via `pip install` (see [README](../../README.ipynb))."
+ ]
},
{
"cell_type": "code",
+ "id": "ef664b14457530fd",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"import sys\n",
"\n",
@@ -96,50 +100,47 @@
"\n",
" await install_packages(\"create_point_defect.ipynb\")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "ef664b14457530fd",
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 1.3. Get input materials\n",
- "Materials are loaded with `get_materials()`."
- ],
+ "id": "919ad7af8dceeedd",
"metadata": {
"collapsed": false
},
- "id": "919ad7af8dceeedd"
+ "source": "### 1.3. Get input materials"
},
{
"cell_type": "code",
+ "id": "be38fdda1984c654",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
"materials = get_materials(globals())"
],
- "metadata": {
- "collapsed": false
- },
- "id": "be38fdda1984c654",
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 1.4. Create and preview Supercell"
- ],
+ "id": "a132fe0ef8bbf0d0",
"metadata": {
"collapsed": false
},
- "id": "a132fe0ef8bbf0d0"
+ "source": [
+ "### 1.4. Create and preview Supercell"
+ ]
},
{
"cell_type": "code",
+ "id": "e2d24109d3068c9e",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"from mat3ra.made.tools.build.supercell import create_supercell\n",
@@ -148,115 +149,121 @@
"supercell = create_supercell(unit_cell, supercell_matrix=SUPERCELL_MATRIX)\n",
"visualize(supercell, repetitions=[1, 1, 1], rotation=\"0x\")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "e2d24109d3068c9e",
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "## 2. Create the Defect\n",
- "### 2.1. Initialize Configuration and Builder parameters"
- ],
+ "id": "5da5b0380583c952",
"metadata": {
"collapsed": false
},
- "id": "5da5b0380583c952"
+ "source": [
+ "## 2. Create Multiple Defects\n",
+ "### 2.1. Prepare defect dictionaries for creation"
+ ]
},
{
"cell_type": "code",
- "source": [
- "from mat3ra.made.tools.build.defect import PointDefectConfiguration\n",
- "from mat3ra.made.tools.build.defect.builders import PointDefectBuilderParameters\n",
- "\n",
- "defect_configurations = [PointDefectConfiguration.from_dict(supercell, defect) for defect in DEFECT_CONFIGS]\n",
- "\n",
- "defect_builder_parameters = PointDefectBuilderParameters(center_defect=False)"
- ],
+ "id": "e385e50ae11ed2b9",
"metadata": {
"collapsed": false
},
- "id": "e385e50ae11ed2b9",
+ "source": [
+ "print(\"Defect configurations:\")\n",
+ "for i, defect_dict in enumerate(DEFECT_CONFIGS):\n",
+ " print(f\"\\n{i+1}. {defect_dict['type'].upper()}:\")\n",
+ " print(f\" - Coordinate: {defect_dict['coordinate']}\")\n",
+ " print(f\" - Resolution method: {defect_dict['placement_method']}\")\n",
+ " if \"element\" in defect_dict:\n",
+ " print(f\" - Element: {defect_dict['element']}\")\n",
+ " \n",
+ "print(f\"\\nTotal defects to create: {len(DEFECT_CONFIGS)}\")"
+ ],
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 2.2. Create the defects"
- ],
+ "id": "489b51f0ee122c48",
"metadata": {
"collapsed": false
},
- "id": "489b51f0ee122c48"
+ "source": [
+ "### 2.2. Create multiple defects using the newer approach"
+ ]
},
{
"cell_type": "code",
- "source": [
- "from mat3ra.made.tools.build.defect import create_defects\n",
- "\n",
- "material_with_defect = create_defects(builder_parameters=defect_builder_parameters,\n",
- " configurations=defect_configurations)"
- ],
+ "id": "a990fa35742d7269",
"metadata": {
"collapsed": false
},
- "id": "a990fa35742d7269",
+ "source": [
+ "from mat3ra.made.tools.build.defect.point.helpers import create_multiple_defects\n",
+ "\n",
+ "material_with_defects = create_multiple_defects(\n",
+ " material=supercell,\n",
+ " defect_dicts=DEFECT_CONFIGS,\n",
+ ")\n",
+ "\n",
+ "print(f\"Original atoms: {len(supercell.basis.elements.ids)}\")\n",
+ "print(f\"Final atoms: {len(material_with_defects.basis.elements.ids)}\")"
+ ],
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "## 3. Visualize Result(s)"
- ],
+ "id": "462549d016073446",
"metadata": {
"collapsed": false
},
- "id": "462549d016073446"
+ "source": [
+ "## 3. Visualize Result(s)"
+ ]
},
{
"cell_type": "code",
+ "id": "509b18661a069e42",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"\n",
"visualize([{\"material\": supercell, \"title\": \"Original material\"},\n",
- " {\"material\": material_with_defect, \"title\": f\"Material with defect\"}],\n",
+ " {\"material\": material_with_defects, \"title\": f\"Material with defects\"}],\n",
" rotation=\"-90x\")\n",
"visualize([{\"material\": supercell, \"title\": \"Original material\"},\n",
- " {\"material\": material_with_defect, \"title\": f\"Material with defect\"}])"
+ " {\"material\": material_with_defects, \"title\": f\"Material with defects\"}])"
],
- "metadata": {
- "collapsed": false
- },
- "id": "509b18661a069e42",
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "## 4. Pass data to the outside runtime"
- ],
+ "id": "d381df29a6bbdd82",
"metadata": {
"collapsed": false
},
- "id": "d381df29a6bbdd82"
+ "source": [
+ "## 4. Pass data to the outside runtime"
+ ]
},
{
"cell_type": "code",
+ "id": "61daa5afcbc078a9",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"from utils.jupyterlite import set_materials\n",
"\n",
- "set_materials([material_with_defect])"
+ "# Set the material name and pass to outside runtime\n",
+ "material_with_defects.name = f\"{unit_cell.name} with {len(DEFECT_CONFIGS)} defects\"\n",
+ "set_materials([material_with_defects])"
],
- "metadata": {
- "collapsed": false
- },
- "id": "61daa5afcbc078a9",
"outputs": [],
"execution_count": null
}
diff --git a/other/materials_designer/create_point_defect_pair.ipynb b/other/materials_designer/create_point_defect_pair.ipynb
index 8f96decdb..9c294c884 100644
--- a/other/materials_designer/create_point_defect_pair.ipynb
+++ b/other/materials_designer/create_point_defect_pair.ipynb
@@ -37,47 +37,46 @@
"id": "5e43ff288847b784"
},
{
+ "metadata": {},
"cell_type": "code",
"source": [
+ "from types import SimpleNamespace\n",
+ "\n",
"# Selected material will be used as a unit cell to create a supercell first.\n",
"SUPERCELL_MATRIX = [[3, 0, 0], [0, 3, 0], [0, 0, 3]]\n",
"\n",
"# List of dictionaries with defect parameters\n",
- "PRIMARY_DEFECT_CONFIG = {\n",
- " \"defect_type\": \"vacancy\",\n",
- " \"approximate_coordinate\": [0.5, 0.5, 0.5],\n",
- " \"use_cartesian_coordinates\": False, # Use cartesian or crystal coordinates\n",
+ "PRIMARY_DEFECT_CONFIG = SimpleNamespace(\n",
+ " defect_type=\"vacancy\",\n",
+ " coordinate=[0.5, 0.5, 0.5], # Approx. coord that will be resolved to the closest site\n",
+ " use_cartesian_coordinates=False, # Use cartesian or crystal coordinates\n",
" # \"site_id\": 0, # Index of the atom in the host material\n",
" # \"coordinate\": None, # Exact position (override the approximate coordinate)\n",
- "}\n",
+ ")\n",
"\n",
- "SECONDARY_DEFECT_CONFIG = {\n",
- " \"defect_type\": \"substitution\",\n",
- " \"approximate_coordinate\": [0.55, 0.55, 0.55],\n",
- " \"chemical_element\": \"C\",\n",
- " # \"site_id\": 0,\n",
- " # \"coordinate\": None,\n",
- "}"
+ "SECONDARY_DEFECT_CONFIG = SimpleNamespace(\n",
+ " defect_type=\"substitution\",\n",
+ " approximate_coordinate=[0.15, 0.15, 0.15], # Approx. coord that will be resolved to the closest site\n",
+ " chemical_element=\"C\", # Element to substitute\n",
+ " # \"site_id\": 0, # Index of the atom in the host material\n",
+ " # \"coordinate\": None, # Exact position (override the approximate coordinate)\n",
+ ")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "9d8b1890b34d850a",
+ "id": "71f275fbc0163e6f",
"outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
"source": [
"### 1.2. Install Packages\n",
"The step executes only in Pyodide environment. For other environments, the packages should be installed via `pip install` (see [README](../../README.ipynb))."
],
- "metadata": {
- "collapsed": false
- },
- "id": "bb64de5ff32649f8"
+ "id": "709d92aa693bd65f"
},
{
+ "metadata": {},
"cell_type": "code",
"source": [
"import sys\n",
@@ -91,10 +90,7 @@
"\n",
" await install_packages(\"create_point_defect.ipynb\")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "ef664b14457530fd",
+ "id": "d499bc9a7f6855f7",
"outputs": [],
"execution_count": null
},
@@ -162,63 +158,38 @@
"id": "5da5b0380583c952"
},
{
+ "metadata": {},
"cell_type": "code",
"source": [
- "from mat3ra.made.tools.build.defect.configuration import PointDefectPairConfiguration, PointDefectConfiguration\n",
- "from mat3ra.made.tools.build.defect.builders import PointDefectBuilderParameters\n",
- "\n",
- "primary_defect_configuration = PointDefectConfiguration.from_dict(supercell, PRIMARY_DEFECT_CONFIG)\n",
- "secondary_defect_configuration = PointDefectConfiguration.from_dict(supercell, SECONDARY_DEFECT_CONFIG)\n",
- "\n",
- "point_defect_pair_configuration = PointDefectPairConfiguration(\n",
- " primary_defect_configuration=primary_defect_configuration,\n",
- " secondary_defect_configuration=secondary_defect_configuration\n",
- ")\n",
- "\n",
- "defect_builder_parameters = PointDefectBuilderParameters(center_defect=False)"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "e385e50ae11ed2b9",
- "outputs": [],
- "execution_count": null
- },
- {
- "cell_type": "markdown",
- "source": [
- "### 2.2. Create the defects"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "489b51f0ee122c48"
- },
- {
- "cell_type": "code",
- "source": [
- "from mat3ra.made.tools.build.defect.builders import PointDefectPairBuilder\n",
- "\n",
- "material_with_defect = PointDefectPairBuilder(defect_builder_parameters).get_material(point_defect_pair_configuration)"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "a990fa35742d7269",
+ "from mat3ra.made.tools.build.defect.pair_defect.helpers import create_pair_defect\n",
+ "\n",
+ "material_with_defect = create_pair_defect(\n",
+ " material=supercell,\n",
+ " defect_type_1=PRIMARY_DEFECT_CONFIG.defect_type,\n",
+ " coordinate_1=PRIMARY_DEFECT_CONFIG.coordinate,\n",
+ " element_1=PRIMARY_DEFECT_CONFIG.chemical_element if hasattr(PRIMARY_DEFECT_CONFIG, \"chemical_element\") else None,\n",
+ " placement_method_1=PRIMARY_DEFECT_CONFIG.placement_method if hasattr(PRIMARY_DEFECT_CONFIG,\n",
+ " 'placement_method') else None,\n",
+ " defect_type_2=SECONDARY_DEFECT_CONFIG.defect_type,\n",
+ " coordinate_2=SECONDARY_DEFECT_CONFIG.approximate_coordinate,\n",
+ " element_2=SECONDARY_DEFECT_CONFIG.chemical_element if hasattr(SECONDARY_DEFECT_CONFIG,\n",
+ " \"chemical_element\") else None,\n",
+ " placement_method_2=SECONDARY_DEFECT_CONFIG.placement_method if hasattr(SECONDARY_DEFECT_CONFIG,\n",
+ " 'placement_method') else None,\n",
+ ")"
+ ],
+ "id": "c4f50fb621da6474",
"outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
- "source": [
- "## 3. Visualize Result(s)"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "462549d016073446"
+ "source": "## 3. Visualize Result(s)",
+ "id": "ae5f5d5e9be9113"
},
{
+ "metadata": {},
"cell_type": "code",
"source": [
"from utils.visualize import visualize_materials as visualize\n",
@@ -229,10 +200,7 @@
"visualize([{\"material\": supercell, \"title\": \"Original material\"},\n",
" {\"material\": material_with_defect, \"title\": f\"Material with defect\"}])"
],
- "metadata": {
- "collapsed": false
- },
- "id": "509b18661a069e42",
+ "id": "8308ef3260816859",
"outputs": [],
"execution_count": null
},
diff --git a/other/materials_designer/create_slab.ipynb b/other/materials_designer/create_slab.ipynb
index fde1ea3fc..c0235d5a1 100644
--- a/other/materials_designer/create_slab.ipynb
+++ b/other/materials_designer/create_slab.ipynb
@@ -51,7 +51,9 @@
"USE_ORTHOGONAL_C = True\n",
"USE_CONVENTIONAL_CELL = True\n",
"\n",
- "# Index of the termination to be selected\n",
+ "# Stoichiometric formula of the slab termination to be used.\n",
+ "SLAB_TERMINATION_FORMULA = None\n",
+ "# if None, the index of all possible terminations will be used\n",
"TERMINATION_INDEX = 0"
],
"metadata": {
@@ -250,11 +252,15 @@
{
"cell_type": "code",
"source": [
+ "from mat3ra.made.tools.build.slab.termination_utils import select_slab_termination\n",
"from utils.io import ui_prompt_select_array_element_by_index, ui_prompt_select_array_element_by_index_pyodide\n",
"\n",
"termination_index = TERMINATION_INDEX\n",
- "\n",
"termination = slab_terminations[termination_index]\n",
+ "\n",
+ "if SLAB_TERMINATION_FORMULA:\n",
+ " termination = select_slab_termination(slab_terminations, SLAB_TERMINATION_FORMULA)\n",
+ "\n",
"if IS_TERMINATIONS_SELECTION_INTERACTIVE:\n",
" if sys.platform == \"emscripten\":\n",
" termination = await ui_prompt_select_array_element_by_index_pyodide(slab_terminations, element_name=\"termination\")\n",
@@ -302,24 +308,6 @@
"outputs": [],
"execution_count": null
},
- {
- "metadata": {},
- "cell_type": "markdown",
- "source": "### 3.2. Create slab supercell",
- "id": "677536f3b6243679"
- },
- {
- "metadata": {},
- "cell_type": "code",
- "source": [
- "from mat3ra.made.tools.operations.core.unary import supercell\n",
- "\n",
- "slab_supercell = supercell(slab, XY_SUPERCELL_MATRIX)"
- ],
- "id": "b67c1b26078499fd",
- "outputs": [],
- "execution_count": null
- },
{
"cell_type": "markdown",
"source": "## 4. Visualize the resulting slab",
@@ -330,7 +318,7 @@
},
{
"cell_type": "code",
- "source": "visualize(slab_supercell, repetitions=[1, 1, 1], rotation=\"0x\")",
+ "source": "visualize(slab, repetitions=[1, 1, 1], rotation=\"0x\")",
"metadata": {
"collapsed": false
},
@@ -352,7 +340,7 @@
"cell_type": "code",
"source": [
"from utils.jupyterlite import set_materials\n",
- "set_materials(slab_supercell)"
+ "set_materials(slab)"
],
"metadata": {
"collapsed": false
diff --git a/other/materials_designer/create_supercell.ipynb b/other/materials_designer/create_supercell.ipynb
index a346210eb..b1a69eff4 100644
--- a/other/materials_designer/create_supercell.ipynb
+++ b/other/materials_designer/create_supercell.ipynb
@@ -32,7 +32,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"SUPERCELL_MATRIX = [\n",
" [3, 0, 0], \n",
@@ -47,7 +46,8 @@
"collapsed": false
},
"id": "e93f72e7c37dea10",
- "execution_count": 0
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -62,7 +62,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"import sys\n",
"\n",
@@ -78,7 +77,8 @@
"collapsed": false
},
"id": "9eb0650f7183279c",
- "execution_count": 0
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -92,7 +92,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
@@ -103,7 +102,8 @@
"collapsed": false
},
"id": "4b72580121ca40d0",
- "execution_count": 0
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -117,7 +117,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.visualize import visualize_materials as visualize\n",
"repetitions = SCALING_FACTOR if SCALING_FACTOR else [3, 3, 1]\n",
@@ -128,7 +127,8 @@
"collapsed": false
},
"id": "d3cba46f185c1a1b",
- "execution_count": 0
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -142,7 +142,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from mat3ra.made.tools.build.supercell import create_supercell\n",
"\n",
@@ -155,7 +154,8 @@
"collapsed": false
},
"id": "2795d5bdbbaafbe6",
- "execution_count": 0
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -169,7 +169,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"visualize(supercell, repetitions=[1, 1, 1], rotation=\"0x\")\n",
"visualize(supercell, repetitions=[1, 1, 1], rotation=\"-90x\")"
@@ -178,7 +177,8 @@
"collapsed": false
},
"id": "aea078560283ca95",
- "execution_count": 0
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -192,7 +192,6 @@
},
{
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import set_materials\n",
"set_materials(supercell)"
@@ -201,7 +200,8 @@
"collapsed": false
},
"id": "cdaf612bc6198546",
- "execution_count": 0
+ "outputs": [],
+ "execution_count": null
}
],
"metadata": {
diff --git a/other/materials_designer/create_terrace_defect.ipynb b/other/materials_designer/create_terrace_defect.ipynb
index e0ef7ef11..de4d89fe1 100644
--- a/other/materials_designer/create_terrace_defect.ipynb
+++ b/other/materials_designer/create_terrace_defect.ipynb
@@ -39,6 +39,7 @@
"id": "ff0f33c4e6ac1303"
},
{
+ "metadata": {},
"cell_type": "code",
"source": [
"# Material selection\n",
@@ -56,7 +57,7 @@
" \"miller_indices\": (0, 0, 1),\n",
" \"thickness\": 6,\n",
" \"vacuum\": 10.0,\n",
- " \"use_orthogonal_z\": True,\n",
+ " \"USE_ORTHOGONAL_C\": True,\n",
" \"xy_supercell_matrix\": [[5, 0], [0, 5]]\n",
"}\n",
"\n",
@@ -64,16 +65,9 @@
"SHOW_INTERMEDIATE_STEPS = True\n",
"CELL_REPETITIONS_FOR_VISUALIZATION = [3, 3, 1] # Structure repeat in view"
],
- "metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2025-05-13T22:53:55.899740Z",
- "start_time": "2025-05-13T22:53:55.894773Z"
- }
- },
- "id": "dd6ca344ae34a2d6",
+ "id": "581cb3ccf2a95f8a",
"outputs": [],
- "execution_count": 1
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -101,15 +95,11 @@
" await install_packages(\"\")"
],
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2025-05-13T22:53:56.024643Z",
- "start_time": "2025-05-13T22:53:56.021253Z"
- }
+ "collapsed": false
},
"id": "38574beae9a769cd",
"outputs": [],
- "execution_count": 2
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -122,97 +112,42 @@
"id": "c0eab57550f40708"
},
{
+ "metadata": {},
"cell_type": "code",
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
- "materials = get_materials(globals())"
- ],
- "metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2025-05-13T22:53:56.404034Z",
- "start_time": "2025-05-13T22:53:56.029464Z"
- }
- },
- "id": "f2479655b99cca48",
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "0: 0-Ni\n",
- "1: 1-Graphene\n",
- "2: C2(001)-Ni4(111), Interface\n",
- "3: Ni26 C1, Substitution C Defect\n",
- "4: Ni4(001), termination Ni_P4:mmm_2, Slab\n",
- "5: O8Zr4(011), termination O2_P2:m_1, Slab\n",
- "Retrieved 6 materials.\n"
- ]
- }
+ "materials = get_materials(globals())\n",
+ "material = materials[MATERIAL_INDEX]"
],
- "execution_count": 3
+ "id": "2eed23af0ec63634",
+ "outputs": [],
+ "execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
- "source": [
- "### 1.4. Create a slab if the input material is not a slab"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "4282a853c29a1501"
+ "source": "### 1.4. Create a slab if the input material is not a slab",
+ "id": "2c0d3e29ca42f099"
},
{
+ "metadata": {},
"cell_type": "code",
"source": [
- "from mat3ra.made.tools.build.slab import create_slab_if_not, SlabConfiguration\n",
+ "from mat3ra.made.tools.build.slab.helpers import create_slab_if_not, SlabConfiguration\n",
"\n",
- "default_slab_config = SlabConfiguration(\n",
- " bulk=materials[0],\n",
+ "default_slab_config = SlabConfiguration.from_parameters(\n",
+ " material_or_dict=material,\n",
" miller_indices=DEFAULT_SLAB_PARAMETERS[\"miller_indices\"],\n",
" number_of_layers=DEFAULT_SLAB_PARAMETERS[\"thickness\"],\n",
" vacuum=DEFAULT_SLAB_PARAMETERS[\"vacuum\"],\n",
- " use_orthogonal_z=DEFAULT_SLAB_PARAMETERS[\"use_orthogonal_z\"],\n",
- " xy_supercell_matrix=DEFAULT_SLAB_PARAMETERS[\"xy_supercell_matrix\"]\n",
")\n",
"\n",
- "slab = create_slab_if_not(materials[0], default_slab_config)"
- ],
- "metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2025-05-13T22:53:58.127131Z",
- "start_time": "2025-05-13T22:53:56.411318Z"
- }
- },
- "id": "80b7b827c2b390c3",
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "The material is not a slab. Creating a new slab...\n"
- ]
- },
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "/Users/mat3ra/code/GREEN/api-examples/.venv-3.11.2/lib/python3.11/site-packages/spglib/spglib.py:115: DeprecationWarning: dict interface (SpglibDataset['number']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead\n",
- " warnings.warn(\n",
- "/Users/mat3ra/code/GREEN/api-examples/.venv-3.11.2/lib/python3.11/site-packages/spglib/spglib.py:115: DeprecationWarning: dict interface (SpglibDataset['international']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead\n",
- " warnings.warn(\n",
- "/Users/mat3ra/code/GREEN/api-examples/.venv-3.11.2/lib/python3.11/site-packages/spglib/spglib.py:115: DeprecationWarning: dict interface (SpglibDataset['wyckoffs']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead\n",
- " warnings.warn(\n",
- "/Users/mat3ra/code/GREEN/api-examples/.venv-3.11.2/lib/python3.11/site-packages/spglib/spglib.py:115: DeprecationWarning: dict interface (SpglibDataset['equivalent_atoms']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead\n",
- " warnings.warn(\n",
- "/Users/mat3ra/code/GREEN/api-examples/.venv-3.11.2/lib/python3.11/site-packages/spglib/spglib.py:115: DeprecationWarning: dict interface (SpglibDataset['rotations']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead\n",
- " warnings.warn(\n"
- ]
- }
+ "slab = create_slab_if_not(material, default_slab_config)"
],
- "execution_count": 4
+ "id": "92ad17e2b0032fda",
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -235,51 +170,11 @@
" visualize_materials(slab, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION, rotation=\"-90x\")"
],
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2025-05-13T22:54:00.098213Z",
- "start_time": "2025-05-13T22:53:58.147449Z"
- }
+ "collapsed": false
},
"id": "16bb968a93de4b9",
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Initial slab structure:\n"
- ]
- },
- {
- "data": {
- "text/plain": [
- "GridBox(children=(VBox(children=(Label(value='Ni600 - Material - rotation: 0x,0y,0z', layout=Layout(align_self…"
- ],
- "application/vnd.jupyter.widget-view+json": {
- "version_major": 2,
- "version_minor": 0,
- "model_id": "5d8f3702971441c0948961611e5b5e05"
- }
- },
- "metadata": {},
- "output_type": "display_data"
- },
- {
- "data": {
- "text/plain": [
- "GridBox(children=(VBox(children=(Label(value='Ni600 - Material - rotation: -90x', layout=Layout(align_self='ce…"
- ],
- "application/vnd.jupyter.widget-view+json": {
- "version_major": 2,
- "version_minor": 0,
- "model_id": "513069d61748466dbeb41e1b657551dc"
- }
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
- "execution_count": 5
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -295,44 +190,33 @@
{
"cell_type": "code",
"source": [
- "from mat3ra.made.tools.build.defect.builders import TerraceSlabDefectConfiguration, TerraceSlabDefectBuilder\n",
+ "from mat3ra.made.tools.build.defect.terrace.helpers import create_terrace\n",
"\n",
- "config = TerraceSlabDefectConfiguration(\n",
- " crystal=slab,\n",
+ "terrace_slab = create_terrace(\n",
+ " slab=slab,\n",
" cut_direction=CUT_DIRECTION,\n",
" pivot_coordinate=PIVOT_COORDINATE,\n",
" number_of_added_layers=NUMBER_OF_ADDED_LAYERS,\n",
" use_cartesian_coordinates=USE_CARTESIAN_COORDINATES,\n",
" rotate_to_match_pbc=ROTATE_TO_MATCH_PBC\n",
- ")\n",
- "\n",
- "builder = TerraceSlabDefectBuilder()"
+ ")\n"
],
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2025-05-13T22:54:00.133631Z",
- "start_time": "2025-05-13T22:54:00.107036Z"
- }
+ "collapsed": false
},
"id": "c318fd03c7e667df",
"outputs": [],
- "execution_count": 6
+ "execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
- "source": [
- "### 2.2. Generate terrace defect\n"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "b9df79c67a870181"
+ "source": "## 2.2. Print the parameters of the created terrace defect",
+ "id": "8547862478ab0c7f"
},
{
"cell_type": "code",
"source": [
- "terrace_slab = builder.get_material(config)\n",
"\n",
"print(\"\\nTerrace defect created with:\")\n",
"print(f\"Cut direction: {CUT_DIRECTION}\")\n",
@@ -341,28 +225,11 @@
"print(f\"Number of atoms: {len(terrace_slab.basis.elements.ids)}\")"
],
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2025-05-13T22:54:00.552490Z",
- "start_time": "2025-05-13T22:54:00.226564Z"
- }
+ "collapsed": false
},
"id": "256bc04ff0aa1810",
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "\n",
- "Terrace defect created with:\n",
- "Cut direction: [1, 0, 0]\n",
- "Pivot point: [0.5, 0.5, 0.5]\n",
- "Added layers: 1\n",
- "Number of atoms: 654\n"
- ]
- }
- ],
- "execution_count": 7
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -382,51 +249,11 @@
"visualize_materials(terrace_slab, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION, rotation=\"-90x\")"
],
"metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2025-05-13T22:54:02.576772Z",
- "start_time": "2025-05-13T22:54:00.605512Z"
- }
+ "collapsed": false
},
"id": "4ffdd8589b02de16",
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Final structure with terrace:\n"
- ]
- },
- {
- "data": {
- "text/plain": [
- "GridBox(children=(VBox(children=(Label(value='Ni654 - Material - rotation: 0x,0y,0z', layout=Layout(align_self…"
- ],
- "application/vnd.jupyter.widget-view+json": {
- "version_major": 2,
- "version_minor": 0,
- "model_id": "7d35ca91ea174c9fb90877b4562f60ba"
- }
- },
- "metadata": {},
- "output_type": "display_data"
- },
- {
- "data": {
- "text/plain": [
- "GridBox(children=(VBox(children=(Label(value='Ni654 - Material - rotation: -90x', layout=Layout(align_self='ce…"
- ],
- "application/vnd.jupyter.widget-view+json": {
- "version_major": 2,
- "version_minor": 0,
- "model_id": "211766fcd37a42fc92982e958157b9ee"
- }
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
- "execution_count": 8
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -439,30 +266,16 @@
"id": "d65865cbab99478"
},
{
+ "metadata": {},
"cell_type": "code",
"source": [
"from utils.jupyterlite import set_materials\n",
"\n",
"set_materials(terrace_slab)"
],
- "metadata": {
- "collapsed": false,
- "ExecuteTime": {
- "end_time": "2025-05-13T22:54:02.627875Z",
- "start_time": "2025-05-13T22:54:02.613998Z"
- }
- },
- "id": "e292358fe4803b4f",
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Data for materials written to uploads/Ni4(001), termination Ni_P4:mmm_2, Slab, 1-step Terrace [1, 0, 0].json\n"
- ]
- }
- ],
- "execution_count": 9
+ "id": "a57ecc6fe9c89ceb",
+ "outputs": [],
+ "execution_count": null
}
],
"metadata": {
diff --git a/other/materials_designer/create_twisted_interface_with_commensurate_lattices.ipynb b/other/materials_designer/create_twisted_interface_with_commensurate_lattices.ipynb
index b1777af4f..ba0593dbe 100644
--- a/other/materials_designer/create_twisted_interface_with_commensurate_lattices.ipynb
+++ b/other/materials_designer/create_twisted_interface_with_commensurate_lattices.ipynb
@@ -2,10 +2,14 @@
"cells": [
{
"cell_type": "markdown",
+ "id": "536d623ca076bbdd",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
" # Create a Twisted Interface with Commensurate Lattices\n",
"\n",
- "Use commensurate lattice matching algorithm to create twisted interfaces between two materials.\n",
+ "Use the `create_commensurate_interface` function to create twisted interfaces between two materials with commensurate lattice matching.\n",
"\n",
"Usage
\n",
"\n",
@@ -19,39 +23,41 @@
"\n",
"1. Prepare the Environment: Set up the notebook and install packages, preview the input materials\n",
"1. Create and visualize the initial materials\n",
- "1. Generate twisted interfaces with commensurate lattice matching\n",
- "1. Select the interface with the desired twist angle and visualize it\n",
+ "1. Create a slab from the input material using `create_slab`\n",
+ "1. Generate twisted interface using `create_commensurate_interface` with the specified parameters\n",
+ "1. Visualize the final twisted interface\n",
"\n",
"## Notes\n",
"\n",
- "1. We perform commensurate lattice matching to find valid supercells that achieve the desired twist angle.\n",
- "1. When the matching is finished, interfaces with angles close to the target are presented.\n",
- "1. The algorithm searches for supercell matrices within specified size limits.\n",
+ "1. We first create a slab from the input material using specified Miller indices.\n",
+ "1. The `create_commensurate_interface` function performs commensurate lattice matching to find valid supercells.\n",
+ "1. The function searches for supercell matrices within specified size limits to achieve the target twist angle.\n",
+ "1. The interface is created with a specified gap between the twisted layers.\n",
+ "1. This approach follows the same pattern as the test suite for reliable results.\n",
"1. For more information, see [Introduction](Introduction.ipynb)\n"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "536d623ca076bbdd"
+ ]
},
{
"cell_type": "markdown",
+ "id": "cc65bd914eecf844",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"## 1. Prepare the Environment\n",
"### 1.1. Set up the notebook\n",
"Set the following flags to control the notebook behavior\n"
- ],
- "metadata": {
- "collapsed": false
- },
- "id": "cc65bd914eecf844"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "be4987fdf0286ebb",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"# Material selection and basic parameters\n",
- "FILM_INDEX = 0# Index in the list of materials, to access as materials[FILM_INDEX]\n",
+ "FILM_INDEX = 0 # Index in the list of materials, to access as materials[FILM_INDEX]\n",
"SUBSTRATE_INDEX = None # Can be None to use same material as film\n",
"\n",
"# Twisted interface parameters\n",
@@ -59,35 +65,43 @@
"INTERFACE_DISTANCE = 3.0 # in Angstroms\n",
"INTERFACE_VACUUM = 20.0 # in Angstroms\n",
"\n",
- "# Search algorithm parameters\n",
- "MAX_REPETITION = 6 # Maximum supercell matrix element value\n",
+ "# Commensurate interface parameters (following the test pattern)\n",
"ANGLE_TOLERANCE = 2.5 # in degrees\n",
+ "MAX_SUPERCELL_MATRIX_INT = 6 # Maximum supercell matrix element value\n",
"RETURN_FIRST_MATCH = True # If True, returns first solution within tolerance\n",
"\n",
+ "# Slab creation parameters\n",
+ "MILLER_INDICES = (0, 0, 1) # Miller indices for slab creation\n",
+ "NUMBER_OF_LAYERS = 1 # Number of layers in the slab\n",
+ "USE_CONVENTIONAL_CELL = True\n",
+ "USE_ORTHOGONAL_C = True\n",
+ "\n",
+ "STACKING_DIRECTION = \"z\" # Stacking direction for the slab, can be \"x\", \"y\", or \"z\"\n",
+ "\n",
"# Visualization parameters\n",
"SHOW_INTERMEDIATE_STEPS = True\n",
"VISUALIZE_REPETITIONS = [3, 3, 1]"
],
- "metadata": {
- "collapsed": false
- },
- "id": "be4987fdf0286ebb",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 1.2. Install packages\n",
- "Explanation is [here](under_the_hood.ipynb#1.2.-Install-packages)."
- ],
+ "id": "5ffda79fd5cad69",
"metadata": {
"collapsed": false
},
- "id": "5ffda79fd5cad69"
+ "source": [
+ "### 1.2. Install packages\n",
+ "Explanation is [here](under_the_hood.ipynb#1.2.-Install-packages)."
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "9f851434739f468a",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"import sys\n",
"\n",
@@ -99,51 +113,51 @@
" from mat3ra.utils.jupyterlite.packages import install_packages\n",
" await install_packages(\"\")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "9f851434739f468a",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 1.3. Load and preview input materials\n",
- "Explanation is [here](under_the_hood.ipynb#2.-Data-Exchange)."
- ],
+ "id": "111e138010f911c",
"metadata": {
"collapsed": false
},
- "id": "111e138010f911c"
+ "source": [
+ "### 1.3. Load and preview input materials\n",
+ "Explanation is [here](under_the_hood.ipynb#2.-Data-Exchange)."
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "d3a815612098f191",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
"materials = get_materials(globals())"
],
- "metadata": {
- "collapsed": false
- },
- "id": "d3a815612098f191",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- " ## 2. Prepare Materials\n",
- " ### 2.1. Select and visualize initial materials"
- ],
+ "id": "8a01e2ba7092ecbe",
"metadata": {
"collapsed": false
},
- "id": "8a01e2ba7092ecbe"
+ "source": [
+ " ## 2. Prepare Materials\n",
+ " ### 2.1. Select and visualize initial materials"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "c920d29700ada27a",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"from utils.visualize import visualize_materials\n",
"\n",
@@ -155,139 +169,147 @@
" if substrate is not film:\n",
" visualize_materials(substrate, repetitions=VISUALIZE_REPETITIONS)"
],
- "metadata": {
- "collapsed": false
- },
- "id": "c920d29700ada27a",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "## 3. Generate Twisted Interface\n",
- "### 3.1. Set up interface configuration and builder\n"
- ],
+ "id": "ce38ef341148321",
"metadata": {
"collapsed": false
},
- "id": "ce38ef341148321"
+ "source": [
+ "## 3. Create Twisted Interface\n",
+ "### 3.1. Create slab and commensurate interface\n"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "d48726a8e99c5590",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
- "from mat3ra.made.tools.build.interface.builders import CommensurateLatticeTwistedInterfaceBuilderParameters, \\\n",
- " CommensurateLatticeTwistedInterfaceBuilder\n",
- "from mat3ra.made.tools.build.interface.configuration import TwistedInterfaceConfiguration\n",
+ "from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum\n",
+ "from mat3ra.made.tools.build.slab.helpers import create_slab\n",
+ "from mat3ra.made.tools.build.interface.helpers import create_commensurate_interface\n",
"\n",
- "config = TwistedInterfaceConfiguration(\n",
- " film=film,\n",
- " substrate=film,\n",
- " twist_angle=TARGET_TWIST_ANGLE,\n",
- " distance_z=INTERFACE_DISTANCE\n",
+ "# Create slab from the material\n",
+ "slab = create_slab(\n",
+ " crystal=film,\n",
+ " miller_indices=MILLER_INDICES,\n",
+ " use_conventional_cell=USE_CONVENTIONAL_CELL,\n",
+ " use_orthogonal_c=USE_ORTHOGONAL_C,\n",
+ " number_of_layers=NUMBER_OF_LAYERS,\n",
+ " vacuum=0.0, # No vacuum in the slab initially\n",
")\n",
"\n",
- "params = CommensurateLatticeTwistedInterfaceBuilderParameters(\n",
- " max_supercell_matrix_int=MAX_REPETITION,\n",
- " angle_tolerance=ANGLE_TOLERANCE,\n",
- " return_first_match=RETURN_FIRST_MATCH\n",
- ")\n",
+ "print(f\"Created slab with {len(slab.basis.elements.ids)} atoms\")\n",
"\n",
- "builder = CommensurateLatticeTwistedInterfaceBuilder(build_parameters=params)"
+ "# Create the commensurate twisted interface using the function from the test\n",
+ "interface = create_commensurate_interface(\n",
+ " material=slab,\n",
+ " target_angle=TARGET_TWIST_ANGLE,\n",
+ " angle_tolerance=ANGLE_TOLERANCE,\n",
+ " max_repetition_int=MAX_SUPERCELL_MATRIX_INT,\n",
+ " return_first_match=RETURN_FIRST_MATCH,\n",
+ " direction=AxisEnum[STACKING_DIRECTION], # Stacking direction for the interface\n",
+ " gap=INTERFACE_DISTANCE, # Gap between layers\n",
+ ")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "d48726a8e99c5590",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 3.2. Generate and analyze interfaces\n"
- ],
+ "id": "211084a2225f5e98",
"metadata": {
"collapsed": false
},
- "id": "211084a2225f5e98"
+ "source": [
+ "### 3.2. Interface creation results\n"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
- "source": [
- "from utils.plot import plot_twisted_interface_solutions\n",
- "\n",
- "interfaces = builder.get_materials(config)\n",
- "\n",
- "print(f\"\\nFound {len(interfaces)} possible interface(s)\")\n",
- "for i, interface in enumerate(interfaces):\n",
- " actual_angle = interface.metadata.get(\"actual_twist_angle\", \"unknown\")\n",
- " print(f\"\\nInterface {i+1}:\")\n",
- " print(f\"Actual twist angle: {actual_angle}°\")\n",
- " print(f\"Number of atoms: {len(interface.basis.elements.ids)}\")\n",
- "\n",
- "\n",
- "if len(interfaces) > 0:\n",
- " plot_twisted_interface_solutions(interfaces)"
- ],
+ "id": "51acc60bf57a26d5",
"metadata": {
"collapsed": false
},
- "id": "51acc60bf57a26d5",
+ "source": [
+ "# The interface was created above using create_commensurate_interface\n",
+ "print(\"\\\\nInterface created successfully!\")\n",
+ "print(f\"Target twist angle: {TARGET_TWIST_ANGLE}°\")\n",
+ "print(f\"Number of atoms: {len(interface.basis.elements.ids)}\")\n",
+ "print(f\"Interface name: {interface.name}\")\n",
+ "\n",
+ "# Show intermediate visualization if requested\n",
+ "if SHOW_INTERMEDIATE_STEPS:\n",
+ " from utils.visualize import visualize_materials\n",
+ " print(\"\\\\nVisualizing the created interface:\")\n",
+ " visualize_materials(interface, repetitions=[1, 1, 1])\n",
+ " visualize_materials(interface, repetitions=[1, 1, 1], rotation=\"-90x\")"
+ ],
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "## 4. Preview the selected material\n",
- "By default, the first interface is selected. You can change the selection by changing the `selected_interface` index."
- ],
+ "id": "370d3acc33cb8907",
"metadata": {
"collapsed": false
},
- "id": "370d3acc33cb8907"
+ "source": [
+ "## 4. Preview the selected material\n",
+ "By default, the first interface is selected. You can change the selection by changing the `selected_interface` index."
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "8fa34c8952f76602",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
- "selected_interface = interfaces[0]\n",
- "actual_angle = selected_interface.metadata.get(\"build\").get(\"configuration\").get(\"actual_twist_angle\")\n",
+ "# The interface is already created above, so just display final results\n",
+ "selected_interface = interface\n",
+ "\n",
+ "print(f\"Final Interface Summary:\")\n",
"print(f\"Target angle: {TARGET_TWIST_ANGLE}°\")\n",
- "print(f\"Actual angle: {actual_angle}°\")\n",
"print(f\"Number of atoms: {len(selected_interface.basis.elements.ids)}\")\n",
+ "print(f\"Cell vectors:\\\\n{selected_interface.basis.cell.vector_arrays}\")\n",
"\n",
+ "# Final visualization\n",
+ "from utils.visualize import visualize_materials\n",
+ "print(\"\\\\nFinal interface visualization:\")\n",
"visualize_materials(selected_interface, repetitions=[1, 1, 1])\n",
"visualize_materials(selected_interface, repetitions=[1, 1, 1], rotation=\"-90x\")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "8fa34c8952f76602",
+ "outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
- "source": [
- "### 5. Pass data to the outside runtime\n"
- ],
+ "id": "87b8655d47b47019",
"metadata": {
"collapsed": false
},
- "id": "87b8655d47b47019"
+ "source": [
+ "### 5. Pass data to the outside runtime\n"
+ ]
},
{
"cell_type": "code",
- "outputs": [],
+ "id": "28bebacd2e299c2c",
+ "metadata": {
+ "collapsed": false
+ },
"source": [
"from utils.jupyterlite import set_materials\n",
"\n",
"set_materials(selected_interface)"
],
- "metadata": {
- "collapsed": false
- },
- "id": "28bebacd2e299c2c",
+ "outputs": [],
"execution_count": null
}
],
diff --git a/other/materials_designer/create_twisted_interface_with_nanoribbons.ipynb b/other/materials_designer/create_twisted_interface_with_nanoribbons.ipynb
index d89f56b42..13410c333 100644
--- a/other/materials_designer/create_twisted_interface_with_nanoribbons.ipynb
+++ b/other/materials_designer/create_twisted_interface_with_nanoribbons.ipynb
@@ -33,115 +33,112 @@
"id": "66b6951c7a25247c"
},
{
+ "metadata": {},
"cell_type": "markdown",
"source": [
"## 1. Prepare the Environment\n",
- "### 1.1. Set up the notebook \n",
- "Set the following flags to control the notebook behavior \n"
+ "### 1.1. Set up the notebook\n",
+ "Set the following flags to control the notebook behavior\n"
],
+ "id": "edec1dd3f8ff0782"
+ },
+ {
"metadata": {
"collapsed": false
},
- "id": "9b35a4b3a796c4ad"
- },
- {
"cell_type": "code",
- "outputs": [],
"source": [
"# Material selection and basic parameters\n",
- "FILM_INDEX = 0 # Index in the list of materials, to access as materials[FILM_INDEX]\n",
+ "FILM_INDEX = 1 # Index in the list of materials, to access as materials[FILM_INDEX]\n",
"SUBSTRATE_INDEX = None # Can be None to use same material as film\n",
"\n",
- "# Interface parameters\n",
- "TWIST_ANGLE = 15.0 # in degrees\n",
+ "# Twisted interface parameters\n",
+ "TARGET_TWIST_ANGLE = 17.9 # in degrees\n",
"INTERFACE_DISTANCE = 3.0 # in Angstroms\n",
"INTERFACE_VACUUM = 20.0 # in Angstroms\n",
"\n",
"# Nanoribbon parameters\n",
- "RIBBON_WIDTH = 5 # Width of the nanoribbon in unit cells\n",
- "RIBBON_LENGTH = 10 # Length of the nanoribbon in unit cells\n",
- "VACUUM_X = 5.0 # Vacuum along x on both sides, in Angstroms\n",
- "VACUUM_Y = 5.0 # Vacuum along y on both sides, in Angstroms\n",
+ "RIBBON_WIDTH = 3 # Width of the nanoribbon in unit cells\n",
+ "RIBBON_LENGTH = 3 # Length of the nanoribbon in unit cells\n",
+ "VACUUM_WIDTH = 15.0 # Vacuum width around ribbons in Angstroms\n",
+ "VACUUM_LENGTH = 15.0 # Vacuum length around ribbons in Angstroms\n",
+ "VACUUM_X = 2.0 # Additional vacuum along x on both sides, in Angstroms\n",
+ "VACUUM_Y = 2.0 # Additional vacuum along y on both sides, in Angstroms\n",
"\n",
"# Visualization parameters\n",
"SHOW_INTERMEDIATE_STEPS = True\n",
- "VISUALIZE_REPETITIONS = [1, 1, 1]"
+ "VISUALIZE_REPETITIONS = [3, 3, 1]"
],
- "metadata": {
- "collapsed": false
- },
- "id": "aaf8db99c7f77c5c",
+ "id": "746db0506f54aeb1",
+ "outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
"source": [
"### 1.2. Install packages\n",
- "The step executes only in Pyodide environment. For other environments, the packages should be installed via `pip install` (see [README](../../README.ipynb))."
+ "Explanation is [here](under_the_hood.ipynb#1.2.-Install-packages)."
],
+ "id": "7e386d88600feb21"
+ },
+ {
"metadata": {
"collapsed": false
},
- "id": "eb558b99e13b8fdc"
- },
- {
"cell_type": "code",
- "outputs": [],
"source": [
"import sys\n",
"\n",
"if sys.platform == \"emscripten\":\n",
" import micropip\n",
- " \n",
+ "\n",
" await micropip.install('mat3ra-api-examples', deps=False)\n",
" await micropip.install('mat3ra-utils')\n",
" from mat3ra.utils.jupyterlite.packages import install_packages\n",
" await install_packages(\"\")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "bd2ed90db5f76f9b",
+ "id": "e5ab0c9b90ba9901",
+ "outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
"source": [
- "### 1.3. Load and preview input materials\n"
+ "### 1.3. Load and preview input materials\n",
+ "Explanation is [here](under_the_hood.ipynb#2.-Data-Exchange)."
],
+ "id": "b38044cae8eca705"
+ },
+ {
"metadata": {
"collapsed": false
},
- "id": "f201817580d12456"
- },
- {
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import get_materials\n",
"\n",
"materials = get_materials(globals())"
],
- "metadata": {
- "collapsed": false
- },
- "id": "dcba2976f2baaa55",
+ "id": "d117934379d38f08",
+ "outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
"source": [
- "## 2. Prepare Materials\n",
- "### 2.1. Select and visualize initial materials\n"
+ " ## 2. Prepare Materials\n",
+ " ### 2.1. Select and visualize initial materials"
],
+ "id": "90d5d8e7cf4f4378"
+ },
+ {
"metadata": {
"collapsed": false
},
- "id": "ee9e7669eecf3deb"
- },
- {
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.visualize import visualize_materials\n",
"\n",
@@ -149,105 +146,129 @@
"substrate = materials[SUBSTRATE_INDEX] if SUBSTRATE_INDEX is not None else film\n",
"\n",
"if SHOW_INTERMEDIATE_STEPS:\n",
- " print(\"\\nInitial material structure:\")\n",
- " visualize_materials(film, repetitions=VISUALIZE_REPETITIONS)"
+ " visualize_materials(film, repetitions=VISUALIZE_REPETITIONS)\n",
+ " if substrate is not film:\n",
+ " visualize_materials(substrate, repetitions=VISUALIZE_REPETITIONS)"
],
- "metadata": {
- "collapsed": false
- },
- "id": "27cc97b9bc42e73b",
+ "id": "d934062047d9cef",
+ "outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
"source": [
- "## 3. Generate Nanoribbon Interface\n",
+ "## 3. Generate Twisted Interface\n",
"### 3.1. Set up interface configuration and builder\n"
],
+ "id": "7dc8fddf36069105"
+ },
+ {
"metadata": {
"collapsed": false
},
- "id": "6e7eb48ae2c4a49d"
- },
- {
"cell_type": "code",
- "outputs": [],
"source": [
- "from mat3ra.made.tools.build.interface.builders import NanoRibbonTwistedInterfaceBuilder\n",
- "from mat3ra.made.tools.build.interface.configuration import NanoRibbonTwistedInterfaceConfiguration\n",
+ "from mat3ra.made.tools.build.interface import create_twisted_interface\n",
+ "# Create nanoribbons from the materials first\n",
+ "from mat3ra.made.tools.build.nanoribbon.helpers import create_nanoribbon\n",
"\n",
- "config = NanoRibbonTwistedInterfaceConfiguration(\n",
- " film=film,\n",
- " substrate=substrate,\n",
- " twist_angle=TWIST_ANGLE,\n",
- " distance_z=INTERFACE_DISTANCE,\n",
- " ribbon_width=RIBBON_WIDTH,\n",
- " ribbon_length=RIBBON_LENGTH,\n",
- " vacuum_x=VACUUM_X,\n",
- " vacuum_y=VACUUM_Y\n",
+ "# Create nanoribbons for both materials\n",
+ "nanoribbon1 = create_nanoribbon(\n",
+ " material=film,\n",
+ " width=RIBBON_WIDTH, # Width in unit cells\n",
+ " length=RIBBON_LENGTH, # Length in unit cells\n",
+ " vacuum_width=VACUUM_WIDTH, # Vacuum width in Angstroms\n",
+ " vacuum_length=VACUUM_LENGTH, # Vacuum length in Angstroms\n",
+ ")\n",
+ "\n",
+ "nanoribbon2 = create_nanoribbon(\n",
+ " material=substrate,\n",
+ " width=RIBBON_WIDTH, # Width in unit cells\n",
+ " length=RIBBON_LENGTH, # Length in unit cells\n",
+ " vacuum_width=VACUUM_WIDTH, # Vacuum width in Angstroms\n",
+ " vacuum_length=VACUUM_LENGTH, # Vacuum length in Angstroms\n",
")\n",
"\n",
- "builder = NanoRibbonTwistedInterfaceBuilder()"
+ "# Create the twisted interface using the manual approach\n",
+ "interface = create_twisted_interface(\n",
+ " material1=nanoribbon1,\n",
+ " material2=nanoribbon2,\n",
+ " angle=TARGET_TWIST_ANGLE,\n",
+ " vacuum_x=VACUUM_X,\n",
+ " vacuum_y=VACUUM_Y,\n",
+ " gap=INTERFACE_DISTANCE,\n",
+ ")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "99c0719450f2fbab",
+ "id": "28ed39605a8b29e",
+ "outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
- "source": [
- "### 3.2. Generate and analyze interface\n"
- ],
+ "source": "### 3.2. Generate and analyze interfaces\n",
+ "id": "53ced0bb45a414d5"
+ },
+ {
"metadata": {
"collapsed": false
},
- "id": "3f38902c015ac965"
- },
- {
"cell_type": "code",
- "outputs": [],
"source": [
- "interface = builder.get_material(config)\n",
- "\n",
- "print(\"\\nInterface created successfully!\")\n",
- "print(f\"Twist angle: {TWIST_ANGLE}°\")\n",
+ "# The interface was already created above using the manual approach\n",
+ "print(\"\\\\nInterface created successfully!\")\n",
+ "print(f\"Target twist angle: {TARGET_TWIST_ANGLE}°\")\n",
+ "print(f\"Actual twist angle: {TARGET_TWIST_ANGLE}°\") # Since we set it manually\n",
"print(f\"Number of atoms: {len(interface.basis.elements.ids)}\")\n",
- "print(f\"Cell vectors:\\n{interface.basis.cell.vectors_as_array}\")\n",
+ "print(f\"Interface name: {interface.name}\")\n",
"\n",
+ "# Show intermediate visualization if requested\n",
"if SHOW_INTERMEDIATE_STEPS:\n",
- " visualize_materials(interface, repetitions=VISUALIZE_REPETITIONS)\n",
- " visualize_materials(interface, repetitions=VISUALIZE_REPETITIONS, rotation=\"-90x\")"
+ " from utils.visualize import visualize_materials\n",
+ " print(\"\\\\nVisualizing the created interface:\")\n",
+ " visualize_materials(interface, repetitions=[1, 1, 1])\n",
+ " visualize_materials(interface, repetitions=[1, 1, 1], rotation=\"-90x\")"
],
- "metadata": {
- "collapsed": false
- },
- "id": "5a6e5f0a57746216",
+ "id": "5b234db939623503",
+ "outputs": [],
"execution_count": null
},
{
+ "metadata": {},
"cell_type": "markdown",
"source": [
- "## 4. Pass data to the outside runtime\n"
+ "## 4. Preview the selected material\n",
+ "By default, the first interface is selected. You can change the selection by changing the `selected_interface` index."
],
+ "id": "3deba4978643a165"
+ },
+ {
+ "metadata": {},
+ "cell_type": "markdown",
+ "source": "### 5. Pass data to the outside runtime\n",
+ "id": "b1d073366e81aeaf"
+ },
+ {
"metadata": {
"collapsed": false
},
- "id": "c296c52797efcf29"
- },
- {
"cell_type": "code",
- "outputs": [],
"source": [
"from utils.jupyterlite import set_materials\n",
"\n",
"set_materials(interface)"
],
- "metadata": {
- "collapsed": false
- },
- "id": "6cf7cccac63dca3d",
+ "id": "4660ac6aad47b522",
+ "outputs": [],
+ "execution_count": null
+ },
+ {
+ "metadata": {},
+ "cell_type": "code",
+ "source": "",
+ "id": "b231dde70694dd41",
+ "outputs": [],
"execution_count": null
}
],
diff --git a/other/materials_designer/passivate_edge.ipynb b/other/materials_designer/passivate_edge.ipynb
index 31c88e77e..dc218c8a0 100644
--- a/other/materials_designer/passivate_edge.ipynb
+++ b/other/materials_designer/passivate_edge.ipynb
@@ -34,8 +34,9 @@
]
},
{
- "metadata": {},
"cell_type": "markdown",
+ "id": "f63b28f159207878",
+ "metadata": {},
"source": [
"## 1. Prepare the Environment\n",
"### 1.1. Set up the notebook\n",
@@ -43,12 +44,12 @@
"Coordination search radius shown on the image below:\n",
"\n",
"![\"Coordination](\"https://github.com/Exabyte-io/documentation/raw/88451ce38b0f57f804dcb5010a1a95bb9b9e50bc/images/notebooks/coordination_based_passivation_settings.webp\")
"
- ],
- "id": "f63b28f159207878"
+ ]
},
{
- "metadata": {},
"cell_type": "code",
+ "id": "7e8d8696bb1035e5",
+ "metadata": {},
"source": [
"# Enable interactive selection of coordination threshold\n",
"IS_COORDINATION_SELECTION_INTERACTIVE = False\n",
@@ -63,7 +64,7 @@
"# Undercoordinated atoms search algorithm parameters\n",
"COORDINATION_THRESHOLD = 2 # Coordination threshold, below which passivation is applied to the atom\n",
"COORDINATION_SEARCH_RADIUS = 3.0 # Distance to look for neighbors for coordination, in Angstroms\n",
- "MAX_BONDS_TO_PASSIVATE = 1 # Maximum number of bonds to passivate\n",
+ "NUMBER_OF_BONDS_TO_PASSIVATE = 1 # Number of bonds to passivate per undercoordinated atom\n",
"\n",
"SYMMETRY_TOLERANCE = 0.1 # Tolerance for symmetry analysis of existing bonds\n",
"\n",
@@ -71,7 +72,6 @@
"SHOW_INTERMEDIATE_STEPS = True\n",
"CELL_REPETITIONS_FOR_VISUALIZATION = [1, 1, 1] # Structure repeat in view"
],
- "id": "7e8d8696bb1035e5",
"outputs": [],
"execution_count": null
},
@@ -181,26 +181,24 @@
},
"source": [
"from utils.io import select_coordination_threshold\n",
- "from mat3ra.made.tools.build.passivation import get_unique_coordination_numbers, PassivationConfiguration, \\\n",
- " get_coordination_numbers_distribution\n",
+ "from mat3ra.made.tools.build.passivation.helpers import get_unique_coordination_numbers, get_coordination_numbers_distribution\n",
"\n",
"coordination_search_radius = None # Change this value according to the RDF plot if needed, Angstroms.\n",
- "config = PassivationConfiguration(\n",
- " slab=nanoribbon,\n",
- " passivant=PASSIVANT,\n",
- " bond_length=BOND_LENGTH\n",
- ")\n",
+ "cutoff = coordination_search_radius or COORDINATION_SEARCH_RADIUS\n",
+ "\n",
+ "# Get coordination numbers using the newer approach\n",
"coordination_numbers = get_unique_coordination_numbers(\n",
- " configuration=config,\n",
- " cutoff=coordination_search_radius or COORDINATION_SEARCH_RADIUS\n",
+ " material=nanoribbon,\n",
+ " cutoff=cutoff\n",
")\n",
"print(f\"Unique coordination numbers: {coordination_numbers}\")\n",
"\n",
"cn_distribution = get_coordination_numbers_distribution(\n",
- " configuration=config,\n",
- " cutoff=coordination_search_radius or COORDINATION_SEARCH_RADIUS\n",
+ " material=nanoribbon,\n",
+ " cutoff=cutoff\n",
")\n",
"print(f\"Coordination numbers distribution: {cn_distribution}\")\n",
+ "\n",
"coordination_threshold = COORDINATION_THRESHOLD\n",
"if IS_COORDINATION_SELECTION_INTERACTIVE:\n",
" coordination_threshold = await select_coordination_threshold(\n",
@@ -220,8 +218,8 @@
"collapsed": false
},
"source": [
- "## 3. Create target material\n",
- "### 3.1. Set up passivation configuration and builder\n"
+ "## 3. Create Passivated Material\n",
+ "### 3.1. Set up passivation parameters\n"
]
},
{
@@ -231,17 +229,18 @@
"collapsed": false
},
"source": [
- "from mat3ra.made.tools.build.passivation.builders import CoordinationBasedPassivationBuilder, \\\n",
- " CoordinationBasedPassivationBuilderParameters\n",
+ "passivation_params = {\n",
+ " \"shadowing_radius\": COORDINATION_SEARCH_RADIUS,\n",
+ " \"coordination_threshold\": coordination_threshold,\n",
+ " \"number_of_bonds_to_passivate\": NUMBER_OF_BONDS_TO_PASSIVATE,\n",
+ " \"symmetry_tolerance\": SYMMETRY_TOLERANCE\n",
+ "}\n",
"\n",
- "builder_params = CoordinationBasedPassivationBuilderParameters(\n",
- " shadowing_radius=COORDINATION_SEARCH_RADIUS,\n",
- " coordination_threshold=coordination_threshold,\n",
- " bonds_to_passivate=MAX_BONDS_TO_PASSIVATE,\n",
- " symmetry_tolerance=SYMMETRY_TOLERANCE\n",
- ")\n",
- "\n",
- "builder = CoordinationBasedPassivationBuilder(build_parameters=builder_params)"
+ "print(f\"Passivation parameters:\")\n",
+ "print(f\" Shadowing radius: {passivation_params['shadowing_radius']} Å\")\n",
+ "print(f\" Coordination threshold: {passivation_params['coordination_threshold']}\")\n",
+ "print(f\" Number of bonds to passivate: {passivation_params['number_of_bonds_to_passivate']}\")\n",
+ "print(f\" Symmetry tolerance: {passivation_params['symmetry_tolerance']}\")"
],
"outputs": [],
"execution_count": null
@@ -263,15 +262,21 @@
"collapsed": false
},
"source": [
- "from mat3ra.made.tools.build.passivation import create_passivation\n",
+ "from mat3ra.made.tools.build.passivation.helpers import passivate_dangling_bonds\n",
"\n",
- "passivated_nanoribbon = create_passivation(config, builder)\n",
+ "passivated_nanoribbon = passivate_dangling_bonds(\n",
+ " material=nanoribbon,\n",
+ " passivant=PASSIVANT,\n",
+ " bond_length=BOND_LENGTH,\n",
+ " **passivation_params\n",
+ ")\n",
"\n",
"print(\"\\nPassivation completed:\")\n",
"print(f\"Passivant used: {PASSIVANT}\")\n",
"print(f\"Bond length: {BOND_LENGTH} Å\")\n",
"print(f\"Original atoms: {len(nanoribbon.basis.elements.ids)}\")\n",
- "print(f\"Final atoms: {len(passivated_nanoribbon.basis.elements.ids)}\")"
+ "print(f\"Final atoms: {len(passivated_nanoribbon.basis.elements.ids)}\")\n",
+ "print(f\"Passivant atoms added: {len(passivated_nanoribbon.basis.elements.ids) - len(nanoribbon.basis.elements.ids)}\")"
],
"outputs": [],
"execution_count": null
diff --git a/other/materials_designer/passivate_slab.ipynb b/other/materials_designer/passivate_slab.ipynb
index d736a3a8d..9f4d2d9bb 100644
--- a/other/materials_designer/passivate_slab.ipynb
+++ b/other/materials_designer/passivate_slab.ipynb
@@ -44,20 +44,21 @@
},
{
"cell_type": "code",
- "execution_count": 5,
"id": "92b3518bebdcf547",
"metadata": {
"collapsed": false
},
- "outputs": [],
"source": [
+ "\n",
+ "from mat3ra.made.tools.modify import translate_to_z_level\n",
+ "\n",
"# Material selection\n",
"MATERIAL_INDEX = 0 # Which material to use from input list\n",
"\n",
"# Passivation parameters\n",
"PASSIVANT = \"H\" # Chemical symbol of passivating atom\n",
"BOND_LENGTH = 1.0 # Distance from surface to passivant, in Angstroms\n",
- "SURFACE = \"both\" # Which surface to passivate: \"top\", \"bottom\" or \"both\"\n",
+ "SURFACE = \"top\" # Which surface to passivate: \"top\", \"bottom\" or \"both\"\n",
"\n",
"# Surface detection parameters\n",
"SHADOWING_RADIUS = 2.5 # Radius to exclude subsurface atoms, in Angstroms\n",
@@ -70,14 +71,16 @@
" \"miller_indices\": (0, 0, 1),\n",
" \"thickness\": 3,\n",
" \"vacuum\": 10.0,\n",
- " \"use_orthogonal_z\": True,\n",
+ " \"USE_ORTHOGONAL_C\": True,\n",
" \"xy_supercell_matrix\": [[3, 0], [0, 3]]\n",
"}\n",
"\n",
"# Visualization parameters\n",
"SHOW_INTERMEDIATE_STEPS = True\n",
"CELL_REPETITIONS_FOR_VISUALIZATION = [1, 1, 1] # Structure repeat in view"
- ]
+ ],
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -92,12 +95,10 @@
},
{
"cell_type": "code",
- "execution_count": 6,
"id": "42863fe84bfab53c",
"metadata": {
"collapsed": false
},
- "outputs": [],
"source": [
"import sys\n",
"\n",
@@ -109,7 +110,9 @@
" from mat3ra.utils.jupyterlite.packages import install_packages\n",
"\n",
" await install_packages(\"\")"
- ]
+ ],
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -123,18 +126,18 @@
},
{
"cell_type": "code",
- "execution_count": null,
"id": "a51551f4af6456c7",
"metadata": {
"collapsed": false
},
- "outputs": [],
"source": [
"from utils.jupyterlite import get_materials\n",
"from utils.visualize import visualize_materials\n",
"\n",
"materials = get_materials(globals())"
- ]
+ ],
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -148,32 +151,31 @@
},
{
"cell_type": "code",
- "execution_count": null,
"id": "ad71f877f76f0550",
"metadata": {
"collapsed": false
},
- "outputs": [],
"source": [
- "from mat3ra.made.tools.build.slab import create_slab_if_not, SlabConfiguration\n",
+ "from mat3ra.made.tools.build.slab.helpers import create_slab_if_not, SlabConfiguration\n",
"\n",
"material = materials[MATERIAL_INDEX]\n",
- "default_slab_config = SlabConfiguration(\n",
- " bulk=material,\n",
+ "default_slab_config = SlabConfiguration.from_parameters(\n",
+ " material_or_dict=material,\n",
" miller_indices=DEFAULT_SLAB_PARAMETERS[\"miller_indices\"],\n",
" number_of_layers=DEFAULT_SLAB_PARAMETERS[\"thickness\"],\n",
" vacuum=DEFAULT_SLAB_PARAMETERS[\"vacuum\"],\n",
- " use_orthogonal_z=DEFAULT_SLAB_PARAMETERS[\"use_orthogonal_z\"],\n",
- " xy_supercell_matrix=DEFAULT_SLAB_PARAMETERS[\"xy_supercell_matrix\"]\n",
")\n",
"\n",
"slab = material if BYPASS_SLAB_CREATION else create_slab_if_not(material, default_slab_config)\n",
+ "slab = translate_to_z_level(slab, \"center\")\n",
"\n",
"if SHOW_INTERMEDIATE_STEPS:\n",
" print(\"Initial slab structure:\")\n",
" visualize_materials(slab, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION)\n",
- " visualize_materials(slab, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION, rotation=\"-90x\")"
- ]
+ " visualize_materials(slab, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION, rotation=\"-90x\")\n"
+ ],
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -183,68 +185,36 @@
},
"source": [
"## 2. Create target material\n",
- "### 2.1. Set up passivation configuration and builder\n"
+ "### 2.1. Passivate the slab surface\n"
]
},
{
"cell_type": "code",
- "execution_count": 9,
- "id": "7e26e8e7fb8319a",
+ "id": "a4ed473eb2129ac4",
"metadata": {
"collapsed": false
},
- "outputs": [],
"source": [
- "from mat3ra.made.tools.build.passivation import (\n",
- " PassivationConfiguration,\n",
- " SurfacePassivationBuilder,\n",
- " SurfacePassivationBuilderParameters\n",
- ")\n",
+ "from mat3ra.made.tools.build.passivation.helpers import passivate_surface\n",
+ "from mat3ra.made.tools.enums import SurfaceTypesEnum\n",
"\n",
- "config = PassivationConfiguration(\n",
- " slab=slab,\n",
+ "passivated_slab = passivate_surface(\n",
+ " slab,\n",
" passivant=PASSIVANT,\n",
" bond_length=BOND_LENGTH,\n",
- " surface=SURFACE\n",
- ")\n",
- "\n",
- "builder_params = SurfacePassivationBuilderParameters(\n",
+ " surface=SurfaceTypesEnum[SURFACE.upper()],\n",
" shadowing_radius=SHADOWING_RADIUS,\n",
" depth=DEPTH\n",
")\n",
"\n",
- "builder = SurfacePassivationBuilder(build_parameters=builder_params)"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "2950f29de8bc79b2",
- "metadata": {
- "collapsed": false
- },
- "source": [
- "### 2.2. Generate passivated structure\n"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "a4ed473eb2129ac4",
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
- "source": [
- "from mat3ra.made.tools.build.passivation import create_passivation\n",
- "\n",
- "passivated_slab = create_passivation(config, builder)\n",
- "\n",
"print(\"\\nPassivation completed:\")\n",
"print(f\"Passivant used: {PASSIVANT}\")\n",
"print(f\"Bond length: {BOND_LENGTH} Å\")\n",
"print(f\"Surfaces passivated: {SURFACE}\")\n",
"print(f\"Number of atoms: {len(passivated_slab.basis.elements.ids)}\")"
- ]
+ ],
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -258,17 +228,17 @@
},
{
"cell_type": "code",
- "execution_count": null,
"id": "c4b5e1e0ec0ab02a",
"metadata": {
"collapsed": false
},
- "outputs": [],
"source": [
"print(\"Final passivated structure:\")\n",
"visualize_materials(passivated_slab, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION)\n",
"visualize_materials(passivated_slab, repetitions=CELL_REPETITIONS_FOR_VISUALIZATION, rotation=\"-90x\")"
- ]
+ ],
+ "outputs": [],
+ "execution_count": null
},
{
"cell_type": "markdown",
@@ -282,17 +252,17 @@
},
{
"cell_type": "code",
- "execution_count": null,
"id": "d66a15a29d27c6ea",
"metadata": {
"collapsed": false
},
- "outputs": [],
"source": [
"from utils.jupyterlite import set_materials\n",
"\n",
"set_materials(passivated_slab)"
- ]
+ ],
+ "outputs": [],
+ "execution_count": null
}
],
"metadata": {
diff --git a/pyproject.toml b/pyproject.toml
index 1798bed2d..ea9863b98 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,7 +10,7 @@ dependencies = [
"matplotlib>=3.4.1",
"pandas>=1.5.3",
"pymatgen==2024.4.13",
- "mat3ra-made>=2025.4.4.post0",
+ "mat3ra-made@git+https://github.com/Exabyte-io/made.git@ffeb01b29b7bf0ac62efb25c42c7612c9c2dee31",
"mat3ra-utils>=2024.6.11.post0",
]
diff --git a/utils/jupyterlite.py b/utils/jupyterlite.py
index 6abd9ee20..c39aa0a7e 100644
--- a/utils/jupyterlite.py
+++ b/utils/jupyterlite.py
@@ -129,6 +129,7 @@ def get_materials(globals_dict: Optional[Dict] = None) -> List[Any]:
List[Material]: A list of Material objects.
"""
from mat3ra.made.material import Material
+ from mat3ra.made.tools.build import MaterialWithBuildMetadata
if globals_dict is None:
# Get the globals of the caller for correct variable assignment during the execution of data_bridge extension
@@ -142,7 +143,12 @@ def get_materials(globals_dict: Optional[Dict] = None) -> List[Any]:
get_data("materials_in", globals_dict)
if "materials_in" in globals_dict and globals_dict["materials_in"]:
- materials = [Material.create(item) for item in globals_dict["materials_in"]]
+ materials = []
+ for item in globals_dict["materials_in"]:
+ try:
+ materials.append(MaterialWithBuildMetadata.create(item))
+ except Exception:
+ materials.append(Material.create(item))
log(f"Retrieved {len(materials)} materials.")
return materials
else:
diff --git a/utils/plot.py b/utils/plot.py
index f102ada97..238ec608e 100644
--- a/utils/plot.py
+++ b/utils/plot.py
@@ -1,17 +1,17 @@
from typing import Dict, List, Union
from mat3ra.made.material import Material
+from mat3ra.made.tools.analyze.interface import ZSLMatchHolder
from mat3ra.made.tools.analyze.rdf import RadialDistributionFunction
-from mat3ra.made.tools.build.interface.enums import StrainModes
from mat3ra.utils.jupyterlite.plot import plot_distribution_function, scatter_plot_2d
-def plot_strain_vs_atoms(interfaces: List["Material"], settings: Dict[str, Union[str, int]]) -> None:
+def plot_strain_vs_area(matches: List["ZSLMatchHolder"], settings: Dict[str, Union[str, int]]) -> None:
"""
Plot strain vs number of atoms for interfaces.
Args:
- interfaces: List of interfaces to plot.
+ matches: List of interface matches to plot.
settings: Plot settings.
"""
@@ -20,18 +20,18 @@ def plot_strain_vs_atoms(interfaces: List["Material"], settings: Dict[str, Union
hover_texts = []
trace_names = []
- for index, interface in enumerate(interfaces):
- strain_percentage = interface.metadata[StrainModes.mean_abs_strain] * 100
- num_sites = len(interface.basis.coordinates.values)
+ for index, match in enumerate(matches):
+ strain_percentage = match.total_strain_percentage
+ match_area = match.match_area
x_values.append(strain_percentage)
- y_values.append(num_sites)
- hover_texts.append(f"Index: {index}
Strain: {strain_percentage:.2f}%
Atoms: {num_sites}")
+ y_values.append(match_area)
+ hover_texts.append(f"Index: {index}
Strain: {strain_percentage:.2f}%
Area: {match_area:.2f} Ų")
trace_names.append(f"Index: {index}")
plot_settings = {
"x_title": "Strain (%)",
- "y_title": "Number of atoms",
+ "y_title": "Area (Ų)",
"x_scale": settings["X_SCALE"],
"y_scale": settings["Y_SCALE"],
"height": settings["HEIGHT"],