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Merged
merged 1 commit into from
May 29, 2025
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fix/SOF-7635 cartesian for point defects #228

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186 changes: 38 additions & 148 deletions other/materials_designer/create_point_defect.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -39,40 +39,37 @@
{
"cell_type": "code",
"source": [
"DEFECT_TYPE = \"substitution\" # (e.g. \"vacancy\", \"substitution\", \"interstitial\")\n",
"SITE_ID = None # Site index of the defect\n",
"COORDINATE = None # Position of the defect in crystal coordinates\n",
"APPROXIMATE_COORDINATE = None # Approximate coordinates of the defect in crystal coordinates\n",
"CHEMICAL_ELEMENT = \"C\" # Element to be placed at the site (ignored for vacancy)\n",
"\n",
"# 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\": DEFECT_TYPE,\n",
" \"approximate_coordinate\": [0.0, 0.0, 0.0],\n",
" \"chemical_element\": \"C\",\n",
" # \"site_id\": 0,\n",
" # \"coordinate\": None,\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",
" },\n",
" # Uncomment the following to create multiple defects\n",
"\n",
" # Uncomment the next lines to create more defects\n",
" # {\n",
" # \"defect_type\": \"vacancy\",\n",
" # \"site_id\": 0,\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,
"ExecuteTime": {
"end_time": "2025-05-13T22:53:42.339489Z",
"start_time": "2025-05-13T22:53:42.334226Z"
}
"collapsed": false
},
"id": "9d8b1890b34d850a",
"outputs": [],
"execution_count": 1
"execution_count": null
},
{
"cell_type": "markdown",
Expand Down Expand Up @@ -100,15 +97,11 @@
" await install_packages(\"create_point_defect.ipynb\")"
],
"metadata": {
"collapsed": false,
"ExecuteTime": {
"end_time": "2025-05-13T22:53:42.360804Z",
"start_time": "2025-05-13T22:53:42.358355Z"
}
"collapsed": false
},
"id": "ef664b14457530fd",
"outputs": [],
"execution_count": 2
"execution_count": null
},
{
"cell_type": "markdown",
Expand All @@ -129,28 +122,11 @@
"materials = get_materials(globals())"
],
"metadata": {
"collapsed": false,
"ExecuteTime": {
"end_time": "2025-05-13T22:53:43.047946Z",
"start_time": "2025-05-13T22:53:42.474580Z"
}
"collapsed": false
},
"id": "be38fdda1984c654",
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"0: 0-Ni\n",
"1: 1-Graphene\n",
"2: C2(001)-Ni4(111), Interface\n",
"3: Ni4(001), termination Ni_P4:mmm_2, Slab\n",
"4: O8Zr4(011), termination O2_P2:m_1, Slab\n",
"Retrieved 5 materials.\n"
]
}
],
"execution_count": 3
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
Expand All @@ -173,30 +149,11 @@
"visualize(supercell, repetitions=[1, 1, 1], rotation=\"0x\")"
],
"metadata": {
"collapsed": false,
"ExecuteTime": {
"end_time": "2025-05-13T22:53:45.847490Z",
"start_time": "2025-05-13T22:53:43.138551Z"
}
"collapsed": false
},
"id": "e2d24109d3068c9e",
"outputs": [
{
"data": {
"text/plain": [
"GridBox(children=(VBox(children=(Label(value='Ni27 - Material - rotation: 0x', layout=Layout(align_self='cente…"
],
"application/vnd.jupyter.widget-view+json": {
"version_major": 2,
"version_minor": 0,
"model_id": "cdc432e2a99c46af8bad06e72d376c4a"
}
},
"metadata": {},
"output_type": "display_data"
}
],
"execution_count": 4
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
Expand All @@ -220,15 +177,11 @@
"defect_builder_parameters = PointDefectBuilderParameters(center_defect=False)"
],
"metadata": {
"collapsed": false,
"ExecuteTime": {
"end_time": "2025-05-13T22:53:45.909568Z",
"start_time": "2025-05-13T22:53:45.873079Z"
}
"collapsed": false
},
"id": "e385e50ae11ed2b9",
"outputs": [],
"execution_count": 5
"execution_count": null
},
{
"cell_type": "markdown",
Expand All @@ -245,33 +198,15 @@
"source": [
"from mat3ra.made.tools.build.defect import create_defects\n",
"\n",
"material_with_defect = create_defects(builder_parameters=defect_builder_parameters, configurations=defect_configurations)"
"material_with_defect = create_defects(builder_parameters=defect_builder_parameters,\n",
" configurations=defect_configurations)"
],
"metadata": {
"collapsed": false,
"ExecuteTime": {
"end_time": "2025-05-13T22:53:45.966908Z",
"start_time": "2025-05-13T22:53:45.916257Z"
}
"collapsed": false
},
"id": "a990fa35742d7269",
"outputs": [
{
"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['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['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['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['wyckoffs']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead\n",
" warnings.warn(\n"
]
}
],
"execution_count": 6
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
Expand All @@ -295,44 +230,11 @@
" {\"material\": material_with_defect, \"title\": f\"Material with defect\"}])"
],
"metadata": {
"collapsed": false,
"ExecuteTime": {
"end_time": "2025-05-13T22:53:46.124855Z",
"start_time": "2025-05-13T22:53:45.980978Z"
}
"collapsed": false
},
"id": "509b18661a069e42",
"outputs": [
{
"data": {
"text/plain": [
"GridBox(children=(VBox(children=(Label(value='Ni27 - Original material - rotation: -90x', layout=Layout(align_…"
],
"application/vnd.jupyter.widget-view+json": {
"version_major": 2,
"version_minor": 0,
"model_id": "a8f71c9f02b54a9ab51c4e9e969e56a3"
}
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/plain": [
"GridBox(children=(VBox(children=(Label(value='Ni27 - Original material - rotation: 0x,0y,0z', layout=Layout(al…"
],
"application/vnd.jupyter.widget-view+json": {
"version_major": 2,
"version_minor": 0,
"model_id": "3cd37b2b7bd646dd8922e0970a5bfe39"
}
},
"metadata": {},
"output_type": "display_data"
}
],
"execution_count": 7
"outputs": [],
"execution_count": null
},
{
"cell_type": "markdown",
Expand All @@ -352,23 +254,11 @@
"set_materials([material_with_defect])"
],
"metadata": {
"collapsed": false,
"ExecuteTime": {
"end_time": "2025-05-13T22:53:46.138694Z",
"start_time": "2025-05-13T22:53:46.134037Z"
}
"collapsed": false
},
"id": "61daa5afcbc078a9",
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Data for materials written to uploads/Ni26 C1, Substitution C Defect.json\n"
]
}
],
"execution_count": 8
"outputs": [],
"execution_count": null
}
],
"metadata": {
Expand Down
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