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Merge pull request #157 from Exabyte-io/feature/SOF-7414
feature/SOF-7414 adatom tutorial NB
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‎other/materials_designer/create_adatom_defect.ipynb‎

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@@ -5,7 +5,9 @@
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"source": [
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"# Create adatom defects in a slab material\n",
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"\n",
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"Create an adatom by specifying the chemical element, approximate position on surface and distance z, which will be resolved to:\n",
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"Create an adatom by specifying the chemical element, approximate position on surface and distance z, as well as placement method which will be resolved to:\n",
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"- exact coordinate,\n",
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"- closest site to provided coordinate,\n",
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"- the equidistant position between the closes atoms on the surface according to Voronoi tesselation, \n",
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"- or the crystal site of the next layer that is closest to specified position.\n",
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"\n",
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"outputs": [],
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"source": [
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"DEFECT_TYPE = \"adatom\" \n",
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"PLACEMENT_METHOD = \"equidistant\" # Choose between \"equidistant\", \"crystal_site\", \"closest_site\", and \"coordinate\"\n",
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"CHEMICAL_ELEMENT = \"Si\" # Element to be placed at the site \n",
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"APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5] # Position of the defect in crystal coordinates\n",
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"USE_CARTESIAN_COORDINATES = False # If True, the position is in Cartesian coordinates\n",
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"DISTANCE_Z = 2.0 # Distance of the defect from the surface in Angstrom\n",
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"CHEMICAL_ELEMENT = \"Si\" # Element to be placed at the site \n",
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"\n",
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"# Slab parameters\n",
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"MILLER_INDICES = (1, 1, 1) # Miller indices of the surface\n",
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"SLAB_THICKNESS = 3 # Thickness of the slab in unit cells\n",
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"VACUUM = 6 # Vacuum thickness in Angstrom\n",
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"outputs": [],
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"source": [
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"from mat3ra.made.tools.build.defect import AdatomSlabPointDefectConfiguration\n",
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"from mat3ra.made.tools.build.defect.builders import EquidistantAdatomSlabDefectBuilder, CrystalSiteAdatomSlabDefectBuilder\n",
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"\n",
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"adatom_config = AdatomSlabPointDefectConfiguration(crystal=slab, \n",
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" defect_type=DEFECT_TYPE, \n",
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" placement_method=PLACEMENT_METHOD,\n",
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" chemical_element=CHEMICAL_ELEMENT, \n",
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" position_on_surface=APPROXIMATE_POSITION_ON_SURFACE,\n",
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" distance_z=DISTANCE_Z, \n",
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" position_on_surface=APPROXIMATE_POSITION_ON_SURFACE\n",
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" use_cartesian_coordinates=USE_CARTESIAN_COORDINATES\n",
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")"
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],
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"metadata": {
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"outputs": [],
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"source": [
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"from mat3ra.made.tools.build.defect import create_slab_defect\n",
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"slab_with_adatom_at_specified_position = create_slab_defect(adatom_config)\n",
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"slab_with_adatom_at_equidistant_position = create_slab_defect(adatom_config, EquidistantAdatomSlabDefectBuilder())\n",
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"slab_with_adatom_at_crystal_site = create_slab_defect(adatom_config, CrystalSiteAdatomSlabDefectBuilder())"
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"slab_with_adatom = create_slab_defect(adatom_config)"
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],
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"metadata": {
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"collapsed": false
@@ -225,13 +230,11 @@
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"from utils.visualize import visualize_materials as visualize\n",
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"\n",
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"visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
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" {\"material\": slab_with_adatom_at_equidistant_position, \"title\": f\"Material with adatom defect at equidistant position\"},\n",
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" {\"material\": slab_with_adatom_at_crystal_site, \"title\": f\"Material with adatom defect at crystal site\"}],\n",
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" {\"material\": slab_with_adatom, \"title\": f\"Material with adatom defect at {PLACEMENT_METHOD} position\"}],\n",
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" rotation=\"-90x\"\n",
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" )\n",
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"visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
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" {\"material\": slab_with_adatom_at_equidistant_position, \"title\": f\"Material with adatom defect at equidistant position\"},\n",
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" {\"material\": slab_with_adatom_at_crystal_site, \"title\": f\"Material with adatom defect at crystal site\"}]\n",
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" {\"material\": slab_with_adatom, \"title\": f\"Material with adatom defect at {PLACEMENT_METHOD} position\"}],\n",
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")"
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],
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"metadata": {
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"source": [
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"from utils.jupyterlite import set_materials\n",
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"\n",
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"set_materials([slab_with_adatom_at_equidistant_position, slab_with_adatom_at_crystal_site])"
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"set_materials([slab_with_adatom])"
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],
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"metadata": {
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"collapsed": false

‎other/materials_designer/specific_examples/defect_surface_adatom_graphene.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"source": [
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"# Adatom Defect on Graphene surface\n",
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"\n",
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"## 0. Introduction\n",
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"\n",
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"This tutorial demonstrates creation of metal adatom on graphene hollow site.\n",
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"\n",
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"> **Chan, K. T., Neaton, J. B., & Cohen, M. L. (2008).** \n",
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"> First-principles study of metal adatom adsorption on graphene. Physical Review B, 77(23). \n",
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"> [DOI:10.1103/physrevb.77.235430 ](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.77.235430)\n",
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" \n",
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"\n",
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"Below is the figure 1 from the manuscript that shows the adsorption of metal adatom on graphene hollow site.\n",
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"\n",
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"\n",
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"![Fig 1.](https://i.imgur.com/EByeJg5.png)\n",
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"\n"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "c62d2c5007947f56"
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},
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{
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"cell_type": "markdown",
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"source": [
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"## 1. Prepare the Environment\n",
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"### 1.1. Set up defects parameters \n",
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"Adatom Defect Configuration parameters are described in [Adatom Defect Configuration](https://github.com/Exabyte-io/made/blob/8196b759242551c77d1791bf5bd2f4150763cfef/src/py/mat3ra/made/tools/build/defect/configuration.py#L141).\n"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "4d0772a456c9952c"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"# Name of material to find in Standata\n",
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"MATERIAL_NAME = \"Graphene\"\n",
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"SUPERCELL_MATRIX = [[4, 0, 0], [0, 4, 0], [0, 0, 1]]\n",
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"\n",
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"# Defect parameters\n",
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"DEFECT_TYPE = \"adatom\"\n",
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"PLACEMENT_METHOD = \"coordinate\"\n",
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"# Using crystal coordinates for the defect placement\n",
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"USE_CARTESIAN_COORDINATES = False \n",
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"HOLLOW_SITE_COORDINATE = [1/2, 1/2] # in crystal coordinates\n",
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"BRIDGE_SITE_COORDINATE = [3/8, 1/2] # in crystal coordinates\n",
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"TOP_SITE_COORDINATE = [7/12, 5/12] # in crystal coordinates\n",
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"\n",
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"# Setting data according to Table 1 in the manuscript, distance_z is the `h` from the table.\n",
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"# Uncomment the lines to create the defect for the desired adatom.\n",
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"ADATOM_PARAMETERS = [\n",
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" {\"chemical_element\": \"Li\", \"distance_z\": 1.71, \"position_on_surface\": HOLLOW_SITE_COORDINATE},\n",
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" {\"chemical_element\": \"Na\", \"distance_z\": 2.28, \"position_on_surface\": HOLLOW_SITE_COORDINATE},\n",
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" {\"chemical_element\": \"K\", \"distance_z\": 2.60, \"position_on_surface\": HOLLOW_SITE_COORDINATE},\n",
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" # {\"chemical_element\": \"Ca\", \"distance_z\": 2.29, \"position_on_surface\": HOLLOW_SITE_COORDINATE},\n",
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" # {\"chemical_element\": \"Al\", \"distance_z\": 2.13, \"position_on_surface\": HOLLOW_SITE_COORDINATE},\n",
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" # {\"chemical_element\": \"Ga\", \"distance_z\": 2.20, \"position_on_surface\": HOLLOW_SITE_COORDINATE},\n",
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" # {\"chemical_element\": \"In\", \"distance_z\": 2.45, \"position_on_surface\": HOLLOW_SITE_COORDINATE},\n",
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" {\"chemical_element\": \"Sn\", \"distance_z\": 2.82, \"position_on_surface\": TOP_SITE_COORDINATE},\n",
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" # {\"chemical_element\": \"Ti\", \"distance_z\": 1.80, \"position_on_surface\": HOLLOW_SITE_COORDINATE},\n",
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" # {\"chemical_element\": \"Fe\", \"distance_z\": 1.53, \"position_on_surface\": HOLLOW_SITE_COORDINATE},\n",
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" {\"chemical_element\": \"Pd\", \"distance_z\": 2.21, \"position_on_surface\": BRIDGE_SITE_COORDINATE},\n",
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" # {\"chemical_element\": \"Au\", \"distance_z\": 2.69, \"position_on_surface\": TOP_SITE_COORDINATE},\n",
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"]"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "b5459bac655071be",
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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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"### 1.2. Install Packages\n",
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"The step executes only in Pyodide environment. For other environments, the packages should be installed via `pip install` (see [README](../../README.ipynb))."
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],
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"metadata": {
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"collapsed": false
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},
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"id": "d572e8697122fef5"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"import sys\n",
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"\n",
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"if sys.platform == \"emscripten\":\n",
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" import micropip\n",
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"\n",
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" await micropip.install('mat3ra-api-examples', deps=False)\n",
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" from utils.jupyterlite import install_packages\n",
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"\n",
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" await install_packages(\"create_point_defect.ipynb\", \"../../../config.yml\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "58b0da5bbc87efc6",
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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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"### 1.3. Load input material"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "b342c025f3e369d4"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from mat3ra.standata.materials import Materials\n",
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"from mat3ra.made.material import Material\n",
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"\n",
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"material = Material(Materials.get_by_name_first_match(MATERIAL_NAME))"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "7ebdb82cd32c735c",
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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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"### 1.4. Create and preview Supercell"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "8f459296488702b1"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from utils.visualize import visualize_materials as visualize\n",
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"from mat3ra.made.tools.build.supercell import create_supercell\n",
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"\n",
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"supercell = create_supercell(material, supercell_matrix=SUPERCELL_MATRIX)\n",
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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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},
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"id": "926503f431d18cad",
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"execution_count": null
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},
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{
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"cell_type": "markdown",
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"source": [
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"## 2. Create the Defect\n",
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"### 2.1. Initialize Configuration and Builder parameters"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "2de6554d42e97c9d"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from mat3ra.made.tools.build.defect import AdatomSlabPointDefectConfiguration\n",
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"from mat3ra.made.tools.build.defect.builders import PointDefectBuilderParameters\n",
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"\n",
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"configurations = [AdatomSlabPointDefectConfiguration(crystal=supercell,\n",
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" defect_type=DEFECT_TYPE,\n",
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" placement_method=PLACEMENT_METHOD,\n",
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" chemical_element=adatom_parameters[\"chemical_element\"],\n",
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" distance_z=adatom_parameters[\"distance_z\"],\n",
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" position_on_surface=adatom_parameters[\"position_on_surface\"],\n",
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" use_cartesian_coordinates=USE_CARTESIAN_COORDINATES\n",
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" ) for adatom_parameters in ADATOM_PARAMETERS]\n",
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"\n",
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"defect_builder_parameters = PointDefectBuilderParameters()"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "74bee7e5ba62200a",
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"execution_count": null
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},
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{
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"cell_type": "markdown",
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"source": [
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"### 2.2. Create the defects"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "a0f09aafb5d9f4d1"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from mat3ra.made.tools.build.defect import create_slab_defect\n",
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"\n",
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"materials_with_adatom = [create_slab_defect(config) for config in configurations]"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "6fc8ad13e12845f",
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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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"## 3. Visualize Result(s)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "5ebf2d6bb1a82b9a"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from utils.visualize import visualize_materials as visualize\n",
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"\n",
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"for material_with_defect in materials_with_adatom:\n",
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" title = f\"{material_with_defect.metadata['build']['configuration']['chemical_element']} adatom\"\n",
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" visualize([{\"material\": material_with_defect, \"title\": title}, {\"material\": material_with_defect, \"title\":title, \"rotation\": \"-90x\"}])"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "93a18e3e1d6e3e6e",
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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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"## 4. Download the Results"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "61176790d8d979e0"
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},
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{
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"cell_type": "code",
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"outputs": [],
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"source": [
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"from utils.jupyterlite import download_content_to_file\n",
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"\n",
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"for material_with_defect in materials_with_adatom:\n",
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" download_content_to_file(material_with_defect.to_json(), f\"{material_with_defect.metadata['build']['configuration']['chemical_element']}_adatom.json\")"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "20ab1b4be207428c",
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"execution_count": null
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 2
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython2",
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"version": "2.7.6"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

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