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Merge pull request #228 from Exabyte-io/fix/SOF-7635
fix/SOF-7635 cartesian for point defects
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‎other/materials_designer/create_point_defect.ipynb

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@@ -39,40 +39,37 @@
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{
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"cell_type": "code",
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"source": [
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"DEFECT_TYPE = \"substitution\" # (e.g. \"vacancy\", \"substitution\", \"interstitial\")\n",
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"SITE_ID = None # Site index of the defect\n",
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"COORDINATE = None # Position of the defect in crystal coordinates\n",
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"APPROXIMATE_COORDINATE = None # Approximate coordinates of the defect in crystal coordinates\n",
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"CHEMICAL_ELEMENT = \"C\" # Element to be placed at the site (ignored for vacancy)\n",
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"\n",
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"# Selected material will be used as a unit cell to create a supercell first.\n",
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"SUPERCELL_MATRIX = [[3, 0, 0], [0, 3, 0], [0, 0, 3]]\n",
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"\n",
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"# List of dictionaries with defect parameters\n",
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"DEFECT_CONFIGS = [\n",
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" {\n",
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" \"defect_type\": DEFECT_TYPE,\n",
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" \"approximate_coordinate\": [0.0, 0.0, 0.0],\n",
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" \"chemical_element\": \"C\",\n",
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" # \"site_id\": 0,\n",
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" # \"coordinate\": None,\n",
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" \"defect_type\": \"substitution\", # (e.g. \"vacancy\", \"substitution\", \"interstitial\")\n",
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" \"chemical_element\": \"C\", # Substitution element\n",
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" \"approximate_coordinate\": [0.0, 0.0, 0.0], # Approx. coord that will be resolved to the closest site\n",
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" \"use_cartesian_coordinates\": True, # Use cartesian or crystal coordinates\n",
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" },\n",
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" # Uncomment the following to create multiple defects\n",
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"\n",
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" # Uncomment the next lines to create more defects\n",
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" # {\n",
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" # \"defect_type\": \"vacancy\",\n",
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" # \"site_id\": 0,\n",
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" # \"defect_type\": \"vacancy\", # Remove an atom at a specific site\n",
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" # \"site_id\": 0, # Index of the atom in the host material\n",
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" # },\n",
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" # {\n",
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" # \"defect_type\": \"interstitial\", # Add an atom at an interstitial site\n",
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" # \"coordinate\": [0.25, 0.25, 0.25], # Exact position\n",
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" # \"use_cartesian_coordinates\": False, # Use cartesian or crystal coordinates\n",
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" # \"chemical_element\": \"N\", # Add interstitial atom\n",
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" # }\n",
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"]"
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],
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-05-13T22:53:42.339489Z",
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"start_time": "2025-05-13T22:53:42.334226Z"
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}
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"collapsed": false
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},
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"id": "9d8b1890b34d850a",
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"outputs": [],
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"execution_count": 1
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"execution_count": null
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},
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{
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"cell_type": "markdown",
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" await install_packages(\"create_point_defect.ipynb\")"
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],
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-05-13T22:53:42.360804Z",
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"start_time": "2025-05-13T22:53:42.358355Z"
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}
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"collapsed": false
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},
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"id": "ef664b14457530fd",
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"outputs": [],
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"execution_count": 2
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"execution_count": null
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},
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{
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"cell_type": "markdown",
@@ -129,28 +122,11 @@
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"materials = get_materials(globals())"
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],
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-05-13T22:53:43.047946Z",
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"start_time": "2025-05-13T22:53:42.474580Z"
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}
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"collapsed": false
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},
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"id": "be38fdda1984c654",
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"0: 0-Ni\n",
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"1: 1-Graphene\n",
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"2: C2(001)-Ni4(111), Interface\n",
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"3: Ni4(001), termination Ni_P4:mmm_2, Slab\n",
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"4: O8Zr4(011), termination O2_P2:m_1, Slab\n",
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"Retrieved 5 materials.\n"
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]
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}
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],
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"execution_count": 3
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"outputs": [],
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"execution_count": null
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},
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{
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"cell_type": "markdown",
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"visualize(supercell, repetitions=[1, 1, 1], rotation=\"0x\")"
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],
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-05-13T22:53:45.847490Z",
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"start_time": "2025-05-13T22:53:43.138551Z"
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}
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"collapsed": false
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},
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"id": "e2d24109d3068c9e",
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"outputs": [
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{
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"data": {
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"text/plain": [
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"GridBox(children=(VBox(children=(Label(value='Ni27 - Material - rotation: 0x', layout=Layout(align_self='cente…"
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],
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"application/vnd.jupyter.widget-view+json": {
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"version_major": 2,
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"version_minor": 0,
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"model_id": "cdc432e2a99c46af8bad06e72d376c4a"
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}
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"execution_count": 4
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"outputs": [],
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"execution_count": null
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},
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{
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"cell_type": "markdown",
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"defect_builder_parameters = PointDefectBuilderParameters(center_defect=False)"
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],
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-05-13T22:53:45.909568Z",
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"start_time": "2025-05-13T22:53:45.873079Z"
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}
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"collapsed": false
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},
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"id": "e385e50ae11ed2b9",
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"outputs": [],
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"execution_count": 5
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"execution_count": null
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},
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{
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"cell_type": "markdown",
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"source": [
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"from mat3ra.made.tools.build.defect import create_defects\n",
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"\n",
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"material_with_defect = create_defects(builder_parameters=defect_builder_parameters, configurations=defect_configurations)"
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"material_with_defect = create_defects(builder_parameters=defect_builder_parameters,\n",
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" configurations=defect_configurations)"
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],
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-05-13T22:53:45.966908Z",
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"start_time": "2025-05-13T22:53:45.916257Z"
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}
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"collapsed": false
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},
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"id": "a990fa35742d7269",
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/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",
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" warnings.warn(\n",
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"/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",
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" warnings.warn(\n",
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"/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",
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" warnings.warn(\n",
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"/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",
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" warnings.warn(\n"
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]
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}
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],
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"execution_count": 6
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"outputs": [],
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"execution_count": null
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"cell_type": "markdown",
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" {\"material\": material_with_defect, \"title\": f\"Material with defect\"}])"
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],
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-05-13T22:53:46.124855Z",
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"start_time": "2025-05-13T22:53:45.980978Z"
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}
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"collapsed": false
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},
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"id": "509b18661a069e42",
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"outputs": [
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{
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"data": {
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"text/plain": [
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"GridBox(children=(VBox(children=(Label(value='Ni27 - Original material - rotation: -90x', layout=Layout(align_…"
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],
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"application/vnd.jupyter.widget-view+json": {
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"version_major": 2,
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"version_minor": 0,
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"model_id": "a8f71c9f02b54a9ab51c4e9e969e56a3"
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}
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},
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"metadata": {},
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"output_type": "display_data"
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},
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{
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"data": {
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"text/plain": [
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"GridBox(children=(VBox(children=(Label(value='Ni27 - Original material - rotation: 0x,0y,0z', layout=Layout(al…"
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],
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"application/vnd.jupyter.widget-view+json": {
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"version_major": 2,
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"version_minor": 0,
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"model_id": "3cd37b2b7bd646dd8922e0970a5bfe39"
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}
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"execution_count": 7
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"outputs": [],
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"execution_count": null
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"cell_type": "markdown",
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"set_materials([material_with_defect])"
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],
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-05-13T22:53:46.138694Z",
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"start_time": "2025-05-13T22:53:46.134037Z"
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}
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"collapsed": false
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},
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"id": "61daa5afcbc078a9",
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Data for materials written to uploads/Ni26 C1, Substitution C Defect.json\n"
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]
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}
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],
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"execution_count": 8
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"outputs": [],
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"execution_count": null
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}
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],
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"metadata": {

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