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feat: construct interface between two materials
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@VsevolodX
VsevolodX committed Sep 29, 2023
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"name": "stdout",
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"text": [
"/Users/mat3ra/.pyenv/versions/3.11.4/bin/python3.11\n",
"8.6.13\n"
]
}
],
"source": [
"import sys\n",
"print(sys.executable)\n",
"#!{sys.executable} -m pip install ase\n",
"#!{sys.executable} -m pip install tk\n",
"import tkinter\n",
"print(tkinter.Tcl().eval('info patchlevel'))\n"
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "c34ddf68-341f-4f81-89de-9a314dee52c6",
"metadata": {},
"outputs": [],
"source": [
"from ase.visualize import view\n",
"import ase.build\n",
"show = False\n",
"\n",
"crystal = ase.build.bulk(\"Ni\", cubic=True)\n",
"if show : view(crystal*[4,4,1])\n",
"\n",
"graphene = ase.build.graphene()\n",
"if show : view(graphene*[2,2,1])\n"
]
},
{
"cell_type": "code",
"execution_count": 129,
"id": "fad3fa15-8b61-409e-aedc-a13f8bf83bb5",
"metadata": {},
"outputs": [],
"source": [
"# data\n",
"global data\n",
"substrate_poscars = [\"\"\"Ni4\n",
"1.0\n",
" 3.4751458659480110 0.0000000000000000 0.0000000000000002\n",
" 0.0000000000000006 3.4751458659480110 0.0000000000000002\n",
" 0.0000000000000000 0.0000000000000000 3.4751458659480110\n",
"Ni\n",
"4\n",
"direct\n",
" 0.0000000000000000 0.0000000000000000 0.0000000000000000 Ni\n",
" 0.0000000000000000 0.5000000000000000 0.5000000000000000 Ni\n",
" 0.5000000000000000 0.0000000000000000 0.5000000000000000 Ni\n",
" 0.5000000000000000 0.5000000000000000 0.0000000000000000 Ni\n",
"\"\"\",\n",
"\"\"\"Cu4\n",
"1.0\n",
" 3.5774306715697510 0.0000000000000000 0.0000000000000002\n",
" 0.0000000000000006 3.5774306715697510 0.0000000000000002\n",
" 0.0000000000000000 0.0000000000000000 3.5774306715697510\n",
"Cu\n",
"4\n",
"direct\n",
" 0.0000000000000000 0.0000000000000000 0.0000000000000000 Cu\n",
" 0.0000000000000000 0.5000000000000000 0.5000000000000000 Cu\n",
" 0.5000000000000000 0.0000000000000000 0.5000000000000000 Cu\n",
" 0.5000000000000000 0.5000000000000000 0.0000000000000000 Cu\n",
"\"\"\",\n",
"\"\"\"Au4\n",
"1.0\n",
" 4.1712885314747270 0.0000000000000000 0.0000000000000003\n",
" 0.0000000000000007 4.1712885314747270 0.0000000000000003\n",
" 0.0000000000000000 0.0000000000000000 4.1712885314747270\n",
"Au\n",
"4\n",
"direct\n",
" 0.0000000000000000 0.0000000000000000 0.0000000000000000 Au\n",
" 0.0000000000000000 0.5000000000000000 0.5000000000000000 Au\n",
" 0.5000000000000000 0.0000000000000000 0.5000000000000000 Au\n",
" 0.5000000000000000 0.5000000000000000 0.0000000000000000 Au\n",
"\"\"\",\n",
"\"\"\"Si4 C4\n",
"1.0\n",
" 4.3539932475828609 0.0000000000000000 0.0000000000000003\n",
" 0.0000000000000007 4.3539932475828609 0.0000000000000003\n",
" 0.0000000000000000 0.0000000000000000 4.3539932475828609\n",
"Si C\n",
"4 4\n",
"direct\n",
" 0.7500000000000000 0.2500000000000000 0.7500000000000000 Si4+\n",
" 0.7500000000000000 0.7500000000000000 0.2500000000000000 Si4+\n",
" 0.2500000000000000 0.2500000000000000 0.2500000000000000 Si4+\n",
" 0.2500000000000000 0.7500000000000000 0.7500000000000000 Si4+\n",
" 0.0000000000000000 0.0000000000000000 0.0000000000000000 C4-\n",
" 0.0000000000000000 0.5000000000000000 0.5000000000000000 C4-\n",
" 0.5000000000000000 0.0000000000000000 0.5000000000000000 C4-\n",
" 0.5000000000000000 0.5000000000000000 0.0000000000000000 C4-\n",
"\"\"\"]\n",
"\n",
"material_poscars = [\"\"\"Graphene\n",
"1.0\n",
" 2.467291000\t 0.000000000\t 0.000000000\n",
" -1.233645000\t 2.136737000\t 0.000000000\n",
" 0.000000000\t 0.000000000\t 7.803074000\n",
"C\n",
"2\n",
"direct\n",
" 0.000000000 0.000000000 0.000000000 C\n",
" 0.333333000 0.666667000 0.000000000 C\n",
"\"\"\",\n",
"\"\"\"Au4\n",
"1.0\n",
" 4.1712885314747270 0.0000000000000000 0.0000000000000003\n",
" 0.0000000000000007 4.1712885314747270 0.0000000000000003\n",
" 0.0000000000000000 0.0000000000000000 4.1712885314747270\n",
"Au\n",
"4\n",
"direct\n",
" 0.0000000000000000 0.0000000000000000 0.0000000000000000 Au\n",
" 0.0000000000000000 0.5000000000000000 0.5000000000000000 Au\n",
" 0.5000000000000000 0.0000000000000000 0.5000000000000000 Au\n",
" 0.5000000000000000 0.5000000000000000 0.0000000000000000 Au\n",
"\"\"\"]\n",
"\n",
"substrate_poscar = substrate_poscars[0]\n",
"material_poscar = material_poscars[0]\n",
"data = [substrate_poscar, material_poscar]"
]
},
{
"cell_type": "code",
"execution_count": 149,
"id": "06ac0aac-d41a-4e95-962b-6de7557cf654",
"metadata": {},
"outputs": [],
"source": [
"# settings\n",
"global settings \n",
"settings = {\"slab_settings\": {\"h\":1, \"k\":1, \"l\":0, \"vacuum\":0.5}, \n",
" \"interface_settings\": {\"substrate\":{\"n\":1, \"m\":2}, \"material\":{\"n\": 3, \"m\": 4}}, \n",
" \"supercell_settings\":{\"n\":3, \"m\":3}}"
]
},
{
"cell_type": "code",
"execution_count": 150,
"id": "491ed5a5-5d3d-47c8-9226-211fff34f7e2",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Atoms(symbols='Ni4', pbc=True, cell=[[3.475145865948011, 0.0, 2e-16], [6e-16, 3.475145865948011, 2e-16], [0.0, 0.0, 3.475145865948011]])\n",
"Atoms(symbols='C2', pbc=True, cell=[[2.467291, 0.0, 0.0], [-1.233645, 2.136737, 0.0], [0.0, 0.0, 7.803074]])\n"
]
}
],
"source": [
"from ase import Atoms\n",
"from ase.build import surface\n",
"from ase.io import read, write\n",
"import io\n",
"from operator import itemgetter\n",
"\n",
"def poscar_to_atoms(poscar):\n",
" input = io.StringIO(poscar)\n",
" atoms = read(input, format=\"vasp\")\n",
" return atoms\n",
" \n",
"def write_atoms_to_poscar(atoms) :\n",
" output = io.StringIO()\n",
" write(output, atoms, format=\"vasp\")\n",
" content = output.getvalue()\n",
" output.close()\n",
" return content\n",
"\n",
"class MaterialInterface:\n",
" def __init__(self, substrate, material, settings=None):\n",
" self.substrate = substrate\n",
" self.material = material\n",
" self.settings = {\n",
" \"slab_settings\": {\"h\": 1, \"k\": 0, \"l\": 0, \"layers\": 3, \"vacuum\": 0.5},\n",
" \"interface_settings\": {\"substrate\":{\"n\":1, \"m\":1}, \"material\": {\"n\":1, \"m\":1}, \"distance\": 2.0},\n",
" \"supercell_settings\": {\"n\":1, \"m\":1}\n",
" }\n",
" if settings:\n",
" for key in self.settings.keys():\n",
" if key in settings:\n",
" self.settings[key].update(settings[key])\n",
" self.structure = self.create_structure()\n",
" \n",
" def create_structure(self):\n",
" h, k, l, layers, vacuum = itemgetter('h', 'k', 'l', 'layers','vacuum')(self.settings[\"slab_settings\"])\n",
" \n",
" distance = itemgetter('distance')(self.settings[\"interface_settings\"])\n",
" substrate_supercell = self.settings[\"interface_settings\"][\"substrate\"]\n",
" material_supercell = self.settings[\"interface_settings\"][\"material\"]\n",
" \n",
" slab = surface(self.substrate, (h, k, l), layers, vacuum)\n",
" slab = slab * [substrate_supercell[\"n\"], substrate_supercell[\"m\"], 1]\n",
" material = self.material * [material_supercell[\"n\"], material_supercell[\"m\"], 1]\n",
"\n",
" z_max_slab = max(slab.positions[:, 2])\n",
" z_min_material = min(material.positions[:, 2])\n",
" z_offset = z_max_slab - z_min_material + distance\n",
" material.positions[:, 2] += z_offset\n",
"\n",
" return slab + material\n",
" \n",
" def create_supercell(self):\n",
" n, m = itemgetter(\"n\", \"m\")(self.settings[\"supercell_settings\"])\n",
" self.structure = self.structure * [n, m, 1]\n",
"\n",
" def calculate_strain():\n",
" return \"not implemetned\"\n",
" \n",
" def view(self):\n",
" view(self.structure)\n",
"\n",
"def func() :\n",
" \"\"\"This function is meant to be a gateway to Pyodide in Materials Designer\"\"\"\n",
" \n",
" poscars = globals()[\"data\"]\n",
" settings = globals()[\"settings\"]\n",
" materials = []\n",
" for poscar in poscars :\n",
" print(poscar_to_atoms(poscar))\n",
" materials.append(poscar_to_atoms(poscar))\n",
"\n",
" \n",
" interface = MaterialInterface(materials[0], materials[1], settings)\n",
" write(\"structure.poscar\", interface.structure, format='vasp')\n",
" \n",
" interface.create_supercell()\n",
" view(interface.structure)\n",
"\n",
"func()\n"
]
},
{
"cell_type": "code",
"execution_count": null,
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