{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Building a MatGraphDB Example with MPNearHull Data\n",
"\n",
"In this notebook, we demonstrate how to build a materials graph database using the\n",
"[MatGraphDB](https://github.com/your/matgraphdb) framework with the MPNearHull dataset.\n",
"\n",
"The steps include:\n",
"1. Importing required libraries and setting up configuration paths.\n",
"2. Downloading and extracting the dataset (and raw materials data if needed).\n",
"3. Creating a MatGraphDB instance.\n",
"4. Initializing node generators.\n",
"5. Initializing edge generators.\n",
"6. Verifying the database setup.\n",
"\n",
"Follow along and run each cell to see how the database is constructed."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Setup"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Library imports and paths are set.\n"
]
}
],
"source": [
"import os\n",
"import shutil\n",
"import zipfile\n",
"import gdown\n",
"\n",
"# Get the data directory from the config. You can change this to your own data directory.\n",
"DATA_DIR = os.path.join(\"..\",\"..\",\"data\",\"examples\",\"01\")\n",
"# Define the path to store the raw materials data.\n",
"MATERIALS_PATH = os.path.join(DATA_DIR, \"material\")\n",
"\n",
"MATGRAPHDB_PATH = os.path.join(DATA_DIR, \"MatGraphDB\")\n",
"\n",
"# Define the dataset URLs.\n",
"DATASET_URL = \"https://drive.google.com/uc?id=1zSmEQbV8pNvjWdhFuCwOeoOzvfoS5XKP\"\n",
"\n",
"# Define the URL for the raw materials data.\n",
"RAW_DATASET_URL = \"https://drive.google.com/uc?id=14guJqEK242XgRGEZA-zIrWyg4b-gX5zk\" # (Not used below but available)\n",
"\n",
"# # Define the path to store the raw materials data.\n",
"# RAW_DATASET_ZIP = os.path.join(config.data_dir, \"raw\", \"MPNearHull_v0.0.1_raw.zip\")\n",
"\n",
"# # Define the path to store the dataset.\n",
"# DATASET_ZIP = os.path.join(config.data_dir, \"datasets\", \"MPNearHull_v0.0.1.zip\")\n",
"\n",
"print(\"Library imports and paths are set.\")\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Define Function for Downloading and Extracting Data"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Downloading raw materials data...\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Downloading...\n",
"From (original): https://drive.google.com/uc?id=1zSmEQbV8pNvjWdhFuCwOeoOzvfoS5XKP\n",
"From (redirected): https://drive.google.com/uc?id=1zSmEQbV8pNvjWdhFuCwOeoOzvfoS5XKP&confirm=t&uuid=5bcba796-ff8e-4bb3-bc09-39d3f1136dc1\n",
"To: c:\\Users\\lllang\\Desktop\\Current_Projects\\MatGraphDB\\examples\\notebooks\\materials\\MPNearHull_v0.0.1_raw.zip\n",
"100%|██████████| 632M/632M [00:11<00:00, 53.6MB/s] \n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Extracting raw materials data...\n",
"Raw materials data ready!\n"
]
}
],
"source": [
"def download_raw_materials(mp_materials_path):\n",
" \"\"\"\n",
" Download and extract the raw materials data if it is not already present.\n",
" \"\"\"\n",
" if not os.path.exists(mp_materials_path):\n",
" \n",
" os.makedirs(mp_materials_path, exist_ok=True)\n",
" print(\"Downloading raw materials data...\")\n",
" \n",
" raw_dataset_zip = os.path.join(mp_materials_path, \"MPNearHull_v0.0.1_raw.zip\")\n",
" # Note: Here we use DATASET_URL as in the original code.\n",
" gdown.download(DATASET_URL, output=raw_dataset_zip, quiet=False)\n",
" \n",
" print(\"Extracting raw materials data...\")\n",
" with zipfile.ZipFile(raw_dataset_zip, \"r\") as zip_ref:\n",
" zip_ref.extractall(mp_materials_path)\n",
" \n",
" \n",
" files=os.listdir(mp_materials_path)\n",
" os.remove(raw_dataset_zip)\n",
" mp_nearhull_path = os.path.join(mp_materials_path, \"MPNearHull\")\n",
" tmp_materials_path = os.path.join(mp_nearhull_path, \"nodes\", \"material\")\n",
" materials_files = os.listdir(tmp_materials_path)\n",
" for file in materials_files:\n",
" shutil.move(os.path.join(tmp_materials_path, file), os.path.join(mp_materials_path, file))\n",
" \n",
" shutil.rmtree(mp_nearhull_path)\n",
" print(\"Raw materials data ready!\")\n",
" \n",
"# Optionally, download the raw materials data if you plan to initialize from raw files.\n",
"if not os.path.exists(MATERIALS_PATH):\n",
" download_raw_materials(MATERIALS_PATH)\n",
"else:\n",
" print(\"Raw materials data already exists.\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Initialization"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Initialize a Materials Store"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"============================================================\n",
"NODE STORE SUMMARY\n",
"============================================================\n",
"Node type: material\n",
"• Number of nodes: 80643\n",
"• Number of features: 136\n",
"Storage path: ..\\..\\data\\examples\\01\\material\n",
"\n",
"\n",
"############################################################\n",
"METADATA\n",
"############################################################\n",
"• class: MaterialStore\n",
"• class_module: matgraphdb.materials.nodes.materials\n",
"• node_type: material\n",
"• name_column: id\n",
"\n",
"############################################################\n",
"NODE DETAILS\n",
"############################################################\n",
"\n"
]
}
],
"source": [
"from matgraphdb import MaterialStore\n",
"\n",
"materials_store = MaterialStore(storage_path=MATERIALS_PATH)\n",
"print(materials_store)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Initialize a MatGraphDB Instance"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"============================================================\n",
"GRAPH DATABASE SUMMARY\n",
"============================================================\n",
"Name: MatGraphDB\n",
"Storage path: ..\\..\\data\\examples\\01\\MatGraphDB\n",
"└── Repository structure:\n",
" ├── nodes/ (..\\..\\data\\examples\\01\\MatGraphDB\\nodes)\n",
" ├── edges/ (..\\..\\data\\examples\\01\\MatGraphDB\\edges)\n",
" ├── edge_generators/ (..\\..\\data\\examples\\01\\MatGraphDB\\edge_generators)\n",
" ├── node_generators/ (..\\..\\data\\examples\\01\\MatGraphDB\\node_generators)\n",
" └── graph/ (..\\..\\data\\examples\\01\\MatGraphDB\\graph)\n",
"\n",
"############################################################\n",
"NODE DETAILS\n",
"############################################################\n",
"Total node types: 1\n",
"------------------------------------------------------------\n",
"• Node type: material\n",
" - Number of nodes: 80643\n",
" - Number of features: 136\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
"------------------------------------------------------------\n",
"\n",
"############################################################\n",
"EDGE DETAILS\n",
"############################################################\n",
"Total edge types: 0\n",
"------------------------------------------------------------\n",
"\n",
"############################################################\n",
"NODE GENERATOR DETAILS\n",
"############################################################\n",
"Total node generators: 0\n",
"------------------------------------------------------------\n",
"\n",
"############################################################\n",
"EDGE GENERATOR DETAILS\n",
"############################################################\n",
"Total edge generators: 0\n",
"------------------------------------------------------------\n",
"\n"
]
}
],
"source": [
"\n",
"from matgraphdb import MatGraphDB\n",
"\n",
"if not os.path.exists(MATGRAPHDB_PATH):\n",
" shutil.rmtree(MATGRAPHDB_PATH)\n",
"mdb = MatGraphDB(storage_path=MATGRAPHDB_PATH,materials_store=materials_store)\n",
"\n",
"print(mdb)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Adding Nodes\n",
"\n",
"In this section, we will add the nodes to the MatGraphDB instance. We will be using some of the built-in node generators to add the nodes to the MatGraphDB instance."
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"from matgraphdb.materials.nodes import (\n",
" element, chemenv, crystal_system, magnetic_state, \n",
" oxidation_state, space_group, wyckoff, material_site, material_lattice\n",
")\n",
"\n",
"# Here we define the generator functions and arguments if they are needed. \n",
"# For instance, to get the materials sites and lattices, we need to pass the materials store to the generator function.\n",
"node_generators = [\n",
" {\"generator_func\": element},\n",
" {\"generator_func\": chemenv},\n",
" {\"generator_func\": crystal_system},\n",
" {\"generator_func\": magnetic_state},\n",
" {\"generator_func\": oxidation_state},\n",
" {\"generator_func\": space_group},\n",
" {\"generator_func\": wyckoff},\n",
" {\n",
" \"generator_func\": material_site,\n",
" \"generator_args\": {\"material_store\": mdb.node_stores[\"material\"]},\n",
" },\n",
" {\n",
" \"generator_func\": material_lattice,\n",
" \"generator_args\": {\"material_store\": mdb.node_stores[\"material\"]},\n",
" },\n",
"]\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now we can add the node generators to the MatGraphDB instance. When we add the generator, it will immediately execute and add the nodes to the database."
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Adding node generator: element\n",
"Adding node generator: chemenv\n",
"Adding node generator: crystal_system\n",
"Adding node generator: magnetic_state\n",
"Adding node generator: oxidation_state\n",
"Adding node generator: space_group\n",
"Adding node generator: wyckoff\n",
"Adding node generator: material_site\n",
"Adding node generator: material_lattice\n",
"Node generators have been initialized.\n",
"============================================================\n",
"GRAPH DATABASE SUMMARY\n",
"============================================================\n",
"Name: MatGraphDB\n",
"Storage path: ..\\..\\data\\examples\\01\\MatGraphDB\n",
"└── Repository structure:\n",
" ├── nodes/ (..\\..\\data\\examples\\01\\MatGraphDB\\nodes)\n",
" ├── edges/ (..\\..\\data\\examples\\01\\MatGraphDB\\edges)\n",
" ├── edge_generators/ (..\\..\\data\\examples\\01\\MatGraphDB\\edge_generators)\n",
" ├── node_generators/ (..\\..\\data\\examples\\01\\MatGraphDB\\node_generators)\n",
" └── graph/ (..\\..\\data\\examples\\01\\MatGraphDB\\graph)\n",
"\n",
"############################################################\n",
"NODE DETAILS\n",
"############################################################\n",
"Total node types: 10\n",
"------------------------------------------------------------\n",
"• Node type: material\n",
" - Number of nodes: 80643\n",
" - Number of features: 136\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
"------------------------------------------------------------\n",
"• Node type: element\n",
" - Number of nodes: 118\n",
" - Number of features: 99\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\element\n",
"------------------------------------------------------------\n",
"• Node type: chemenv\n",
" - Number of nodes: 67\n",
" - Number of features: 15\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\chemenv\n",
"------------------------------------------------------------\n",
"• Node type: crystal_system\n",
" - Number of nodes: 7\n",
" - Number of features: 2\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\crystal_system\n",
"------------------------------------------------------------\n",
"• Node type: magnetic_state\n",
" - Number of nodes: 5\n",
" - Number of features: 2\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\magnetic_state\n",
"------------------------------------------------------------\n",
"• Node type: oxidation_state\n",
" - Number of nodes: 19\n",
" - Number of features: 3\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\oxidation_state\n",
"------------------------------------------------------------\n",
"• Node type: space_group\n",
" - Number of nodes: 230\n",
" - Number of features: 2\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\space_group\n",
"------------------------------------------------------------\n",
"• Node type: wyckoff\n",
" - Number of nodes: 1380\n",
" - Number of features: 2\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\wyckoff\n",
"------------------------------------------------------------\n",
"• Node type: material_site\n",
" - Number of nodes: 2545026\n",
" - Number of features: 15\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material_site\n",
"------------------------------------------------------------\n",
"• Node type: material_lattice\n",
" - Number of nodes: 80643\n",
" - Number of features: 12\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material_lattice\n",
"------------------------------------------------------------\n",
"\n",
"############################################################\n",
"EDGE DETAILS\n",
"############################################################\n",
"Total edge types: 0\n",
"------------------------------------------------------------\n",
"\n",
"############################################################\n",
"NODE GENERATOR DETAILS\n",
"############################################################\n",
"Total node generators: 9\n",
"------------------------------------------------------------\n",
"• Generator: element\n",
"Generator Args:\n",
" - generator_func: [<function element at 0x000001E1A2C82C10>]\n",
" - generator_kwargs.base_file: ['C:\\\\Users\\\\lllang\\\\Desktop\\\\Current_Projects\\\\MatGraphDB\\\\matgraphdb\\\\utils\\\\chem_utils\\\\resources\\\\imputed_periodic_table_values.parquet']\n",
" - generator_name: ['element']\n",
" - id: [0]\n",
"Generator Kwargs:\n",
" - base_file: ['C:\\\\Users\\\\lllang\\\\Desktop\\\\Current_Projects\\\\MatGraphDB\\\\matgraphdb\\\\utils\\\\chem_utils\\\\resources\\\\imputed_periodic_table_values.parquet']\n",
"------------------------------------------------------------\n",
"• Generator: chemenv\n",
"Generator Args:\n",
" - generator_func: [<function chemenv at 0x000001E1A2C82D30>]\n",
" - generator_kwargs.base_file: ['C:\\\\Users\\\\lllang\\\\Desktop\\\\Current_Projects\\\\MatGraphDB\\\\matgraphdb\\\\utils\\\\chem_utils\\\\resources\\\\coordination_geometries.parquet']\n",
" - generator_name: ['chemenv']\n",
" - id: [1]\n",
"Generator Kwargs:\n",
" - base_file: ['C:\\\\Users\\\\lllang\\\\Desktop\\\\Current_Projects\\\\MatGraphDB\\\\matgraphdb\\\\utils\\\\chem_utils\\\\resources\\\\coordination_geometries.parquet']\n",
"------------------------------------------------------------\n",
"• Generator: crystal_system\n",
"Generator Args:\n",
" - generator_func: [<function crystal_system at 0x000001E1A2C82E50>]\n",
" - generator_name: ['crystal_system']\n",
" - id: [2]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: magnetic_state\n",
"Generator Args:\n",
" - generator_func: [<function magnetic_state at 0x000001E1A2C82F70>]\n",
" - generator_name: ['magnetic_state']\n",
" - id: [3]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: oxidation_state\n",
"Generator Args:\n",
" - generator_func: [<function oxidation_state at 0x000001E1A2C8D0D0>]\n",
" - generator_name: ['oxidation_state']\n",
" - id: [4]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: space_group\n",
"Generator Args:\n",
" - generator_func: [<function space_group at 0x000001E1A2C8D1F0>]\n",
" - generator_name: ['space_group']\n",
" - id: [5]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: wyckoff\n",
"Generator Args:\n",
" - generator_func: [<function wyckoff at 0x000001E1A2C8D310>]\n",
" - generator_name: ['wyckoff']\n",
" - id: [6]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: material_site\n",
"Generator Args:\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
" - generator_func: [<function material_site at 0x000001E1C487D940>]\n",
" - generator_name: ['material_site']\n",
" - id: [7]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: material_lattice\n",
"Generator Args:\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
" - generator_func: [<function material_lattice at 0x000001E1C487D820>]\n",
" - generator_name: ['material_lattice']\n",
" - id: [8]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"\n",
"############################################################\n",
"EDGE GENERATOR DETAILS\n",
"############################################################\n",
"Total edge generators: 0\n",
"------------------------------------------------------------\n",
"\n"
]
}
],
"source": [
"# Add each node generator to the database.\n",
"for generator in node_generators:\n",
" generator_func = generator.get(\"generator_func\")\n",
" generator_args = generator.get(\"generator_args\", None)\n",
" print(f\"Adding node generator: {generator_func.__name__}\")\n",
" mdb.add_node_generator(generator_func=generator_func, generator_args=generator_args)\n",
"\n",
"print(\"Node generators have been initialized.\")\n",
"\n",
"print(mdb)\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Adding Edges\n",
"\n",
"In this section, we will add the edges to the MatGraphDB instance. We will be using some of the built-in edge generators to add the edges to the MatGraphDB instance."
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Adding edge generator: element_element_neighborsByGroupPeriod\n",
"Adding edge generator: element_oxiState_canOccur\n",
"Adding edge generator: material_chemenv_containsSite\n",
"Adding edge generator: material_crystalSystem_has\n",
"Adding edge generator: material_element_has\n",
"Adding edge generator: material_lattice_has\n",
"Adding edge generator: material_spg_has\n",
"Adding edge generator: element_chemenv_canOccur\n",
"Adding edge generator: spg_crystalSystem_isApart\n",
"Adding edge generator: element_element_bonds\n",
"Edge generators have been initialized.\n",
"============================================================\n",
"GRAPH DATABASE SUMMARY\n",
"============================================================\n",
"Name: MatGraphDB\n",
"Storage path: ..\\..\\data\\examples\\01\\MatGraphDB\n",
"└── Repository structure:\n",
" ├── nodes/ (..\\..\\data\\examples\\01\\MatGraphDB\\nodes)\n",
" ├── edges/ (..\\..\\data\\examples\\01\\MatGraphDB\\edges)\n",
" ├── edge_generators/ (..\\..\\data\\examples\\01\\MatGraphDB\\edge_generators)\n",
" ├── node_generators/ (..\\..\\data\\examples\\01\\MatGraphDB\\node_generators)\n",
" └── graph/ (..\\..\\data\\examples\\01\\MatGraphDB\\graph)\n",
"\n",
"############################################################\n",
"NODE DETAILS\n",
"############################################################\n",
"Total node types: 10\n",
"------------------------------------------------------------\n",
"• Node type: material\n",
" - Number of nodes: 80643\n",
" - Number of features: 136\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
"------------------------------------------------------------\n",
"• Node type: element\n",
" - Number of nodes: 118\n",
" - Number of features: 99\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\element\n",
"------------------------------------------------------------\n",
"• Node type: chemenv\n",
" - Number of nodes: 67\n",
" - Number of features: 15\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\chemenv\n",
"------------------------------------------------------------\n",
"• Node type: crystal_system\n",
" - Number of nodes: 7\n",
" - Number of features: 2\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\crystal_system\n",
"------------------------------------------------------------\n",
"• Node type: magnetic_state\n",
" - Number of nodes: 5\n",
" - Number of features: 2\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\magnetic_state\n",
"------------------------------------------------------------\n",
"• Node type: oxidation_state\n",
" - Number of nodes: 19\n",
" - Number of features: 3\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\oxidation_state\n",
"------------------------------------------------------------\n",
"• Node type: space_group\n",
" - Number of nodes: 230\n",
" - Number of features: 2\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\space_group\n",
"------------------------------------------------------------\n",
"• Node type: wyckoff\n",
" - Number of nodes: 1380\n",
" - Number of features: 2\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\wyckoff\n",
"------------------------------------------------------------\n",
"• Node type: material_site\n",
" - Number of nodes: 2545026\n",
" - Number of features: 15\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material_site\n",
"------------------------------------------------------------\n",
"• Node type: material_lattice\n",
" - Number of nodes: 80643\n",
" - Number of features: 12\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material_lattice\n",
"------------------------------------------------------------\n",
"\n",
"############################################################\n",
"EDGE DETAILS\n",
"############################################################\n",
"Total edge types: 10\n",
"------------------------------------------------------------\n",
"• Edge type: element_element_neighborsByGroupPeriod\n",
" - Number of edges: 391\n",
" - Number of features: 14\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\element_element_neighborsByGroupPeriod\n",
"------------------------------------------------------------\n",
"• Edge type: element_oxiState_canOccur\n",
" - Number of edges: 162\n",
" - Number of features: 8\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\element_oxiState_canOccur\n",
"------------------------------------------------------------\n",
"• Edge type: material_chemenv_containsSite\n",
" - Number of edges: 2542897\n",
" - Number of features: 8\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\material_chemenv_containsSite\n",
"------------------------------------------------------------\n",
"• Edge type: material_crystalSystem_has\n",
" - Number of edges: 80643\n",
" - Number of features: 10\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\material_crystalSystem_has\n",
"------------------------------------------------------------\n",
"• Edge type: material_element_has\n",
" - Number of edges: 270902\n",
" - Number of features: 8\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\material_element_has\n",
"------------------------------------------------------------\n",
"• Edge type: material_lattice_has\n",
" - Number of edges: 80643\n",
" - Number of features: 8\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\material_lattice_has\n",
"------------------------------------------------------------\n",
"• Edge type: material_spg_has\n",
" - Number of edges: 80643\n",
" - Number of features: 10\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\material_spg_has\n",
"------------------------------------------------------------\n",
"• Edge type: element_chemenv_canOccur\n",
" - Number of edges: 270474\n",
" - Number of features: 7\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\element_chemenv_canOccur\n",
"------------------------------------------------------------\n",
"• Edge type: spg_crystalSystem_isApart\n",
" - Number of edges: 230\n",
" - Number of features: 7\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\spg_crystalSystem_isApart\n",
"------------------------------------------------------------\n",
"• Edge type: element_element_bonds\n",
" - Number of edges: 3069943\n",
" - Number of features: 7\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\element_element_bonds\n",
"------------------------------------------------------------\n",
"\n",
"############################################################\n",
"NODE GENERATOR DETAILS\n",
"############################################################\n",
"Total node generators: 9\n",
"------------------------------------------------------------\n",
"• Generator: element\n",
"Generator Args:\n",
" - generator_func: [<function element at 0x000001E1A2C82C10>]\n",
" - generator_kwargs.base_file: ['C:\\\\Users\\\\lllang\\\\Desktop\\\\Current_Projects\\\\MatGraphDB\\\\matgraphdb\\\\utils\\\\chem_utils\\\\resources\\\\imputed_periodic_table_values.parquet']\n",
" - generator_name: ['element']\n",
" - id: [0]\n",
"Generator Kwargs:\n",
" - base_file: ['C:\\\\Users\\\\lllang\\\\Desktop\\\\Current_Projects\\\\MatGraphDB\\\\matgraphdb\\\\utils\\\\chem_utils\\\\resources\\\\imputed_periodic_table_values.parquet']\n",
"------------------------------------------------------------\n",
"• Generator: chemenv\n",
"Generator Args:\n",
" - generator_func: [<function chemenv at 0x000001E1A2C82D30>]\n",
" - generator_kwargs.base_file: ['C:\\\\Users\\\\lllang\\\\Desktop\\\\Current_Projects\\\\MatGraphDB\\\\matgraphdb\\\\utils\\\\chem_utils\\\\resources\\\\coordination_geometries.parquet']\n",
" - generator_name: ['chemenv']\n",
" - id: [1]\n",
"Generator Kwargs:\n",
" - base_file: ['C:\\\\Users\\\\lllang\\\\Desktop\\\\Current_Projects\\\\MatGraphDB\\\\matgraphdb\\\\utils\\\\chem_utils\\\\resources\\\\coordination_geometries.parquet']\n",
"------------------------------------------------------------\n",
"• Generator: crystal_system\n",
"Generator Args:\n",
" - generator_func: [<function crystal_system at 0x000001E1A2C82E50>]\n",
" - generator_name: ['crystal_system']\n",
" - id: [2]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: magnetic_state\n",
"Generator Args:\n",
" - generator_func: [<function magnetic_state at 0x000001E1A2C82F70>]\n",
" - generator_name: ['magnetic_state']\n",
" - id: [3]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: oxidation_state\n",
"Generator Args:\n",
" - generator_func: [<function oxidation_state at 0x000001E1A2C8D0D0>]\n",
" - generator_name: ['oxidation_state']\n",
" - id: [4]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: space_group\n",
"Generator Args:\n",
" - generator_func: [<function space_group at 0x000001E1A2C8D1F0>]\n",
" - generator_name: ['space_group']\n",
" - id: [5]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: wyckoff\n",
"Generator Args:\n",
" - generator_func: [<function wyckoff at 0x000001E1A2C8D310>]\n",
" - generator_name: ['wyckoff']\n",
" - id: [6]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: material_site\n",
"Generator Args:\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
" - generator_func: [<function material_site at 0x000001E1C487D940>]\n",
" - generator_name: ['material_site']\n",
" - id: [7]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: material_lattice\n",
"Generator Args:\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
" - generator_func: [<function material_lattice at 0x000001E1C487D820>]\n",
" - generator_name: ['material_lattice']\n",
" - id: [8]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"\n",
"############################################################\n",
"EDGE GENERATOR DETAILS\n",
"############################################################\n",
"Total edge generators: 10\n",
"------------------------------------------------------------\n",
"• Generator: element_oxiState_canOccur\n",
"Generator Args:\n",
" - element_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\element\n",
" - oxiState_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\oxidation_state\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: material_chemenv_containsSite\n",
"Generator Args:\n",
" - chemenv_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\chemenv\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: material_crystalSystem_has\n",
"Generator Args:\n",
" - crystal_system_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\crystal_system\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: element_element_neighborsByGroupPeriod\n",
"Generator Args:\n",
" - element_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\element\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: material_element_has\n",
"Generator Args:\n",
" - element_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\element\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: material_lattice_has\n",
"Generator Args:\n",
" - lattice_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material_lattice\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: material_spg_has\n",
"Generator Args:\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
" - spg_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\space_group\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: element_chemenv_canOccur\n",
"Generator Args:\n",
" - chemenv_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\chemenv\n",
" - element_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\element\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: spg_crystalSystem_isApart\n",
"Generator Args:\n",
" - crystal_system_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\crystal_system\n",
" - spg_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\space_group\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: element_element_bonds\n",
"Generator Args:\n",
" - element_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\element\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"\n"
]
}
],
"source": [
"from matgraphdb.materials.edges import (\n",
" material_element_has,\n",
" material_lattice_has,\n",
" material_spg_has,\n",
" element_element_neighborsByGroupPeriod,\n",
" element_element_bonds,\n",
" element_oxiState_canOccur,\n",
" material_chemenv_containsSite,\n",
" material_crystalSystem_has,\n",
" element_chemenv_canOccur,\n",
" spg_crystalSystem_isApart,\n",
")\n",
"\n",
"\n",
"\n",
"# List of edge generator configurations.\n",
"edge_generators = [\n",
" {\n",
" \"generator_func\": element_element_neighborsByGroupPeriod,\n",
" \"generator_args\": {\"element_store\": mdb.node_stores[\"element\"]},\n",
" },\n",
" {\n",
" \"generator_func\": element_oxiState_canOccur,\n",
" \"generator_args\": {\n",
" \"element_store\": mdb.node_stores[\"element\"],\n",
" \"oxiState_store\": mdb.node_stores[\"oxidation_state\"],\n",
" },\n",
" },\n",
" {\n",
" \"generator_func\": material_chemenv_containsSite,\n",
" \"generator_args\": {\n",
" \"material_store\": mdb.node_stores[\"material\"],\n",
" \"chemenv_store\": mdb.node_stores[\"chemenv\"],\n",
" },\n",
" },\n",
" {\n",
" \"generator_func\": material_crystalSystem_has,\n",
" \"generator_args\": {\n",
" \"material_store\": mdb.node_stores[\"material\"],\n",
" \"crystal_system_store\": mdb.node_stores[\"crystal_system\"],\n",
" },\n",
" },\n",
" {\n",
" \"generator_func\": material_element_has,\n",
" \"generator_args\": {\n",
" \"material_store\": mdb.node_stores[\"material\"],\n",
" \"element_store\": mdb.node_stores[\"element\"],\n",
" },\n",
" },\n",
" {\n",
" \"generator_func\": material_lattice_has,\n",
" \"generator_args\": {\n",
" \"material_store\": mdb.node_stores[\"material\"],\n",
" \"lattice_store\": mdb.node_stores[\"material_lattice\"],\n",
" },\n",
" },\n",
" {\n",
" \"generator_func\": material_spg_has,\n",
" \"generator_args\": {\n",
" \"material_store\": mdb.node_stores[\"material\"],\n",
" \"spg_store\": mdb.node_stores[\"space_group\"],\n",
" },\n",
" },\n",
" {\n",
" \"generator_func\": element_chemenv_canOccur,\n",
" \"generator_args\": {\n",
" \"element_store\": mdb.node_stores[\"element\"],\n",
" \"chemenv_store\": mdb.node_stores[\"chemenv\"],\n",
" \"material_store\": mdb.node_stores[\"material\"],\n",
" },\n",
" },\n",
" {\n",
" \"generator_func\": spg_crystalSystem_isApart,\n",
" \"generator_args\": {\n",
" \"spg_store\": mdb.node_stores[\"space_group\"],\n",
" \"crystal_system_store\": mdb.node_stores[\"crystal_system\"],\n",
" },\n",
" },\n",
" {\n",
" \"generator_func\": element_element_bonds,\n",
" \"generator_args\": {\n",
" \"element_store\": mdb.node_stores[\"element\"],\n",
" \"material_store\": mdb.node_stores[\"material\"],\n",
" },\n",
" },\n",
"]\n",
"\n",
"\n",
"# Add each edge generator to the database and run them immediately.\n",
"for generator in edge_generators:\n",
" generator_func = generator.get(\"generator_func\")\n",
" generator_args = generator.get(\"generator_args\", None)\n",
" print(f\"Adding edge generator: {generator_func.__name__}\")\n",
" mdb.add_edge_generator(generator_func=generator_func, generator_args=generator_args, run_immediately=True)\n",
"\n",
"print(\"Edge generators have been initialized.\")\n",
"print(mdb)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Verifying the Database\n"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"============================================================\n",
"GRAPH DATABASE SUMMARY\n",
"============================================================\n",
"Name: MatGraphDB\n",
"Storage path: ..\\..\\data\\examples\\01\\MatGraphDB\n",
"└── Repository structure:\n",
" ├── nodes/ (..\\..\\data\\examples\\01\\MatGraphDB\\nodes)\n",
" ├── edges/ (..\\..\\data\\examples\\01\\MatGraphDB\\edges)\n",
" ├── edge_generators/ (..\\..\\data\\examples\\01\\MatGraphDB\\edge_generators)\n",
" ├── node_generators/ (..\\..\\data\\examples\\01\\MatGraphDB\\node_generators)\n",
" └── graph/ (..\\..\\data\\examples\\01\\MatGraphDB\\graph)\n",
"\n",
"############################################################\n",
"NODE DETAILS\n",
"############################################################\n",
"Total node types: 10\n",
"------------------------------------------------------------\n",
"• Node type: material\n",
" - Number of nodes: 80643\n",
" - Number of features: 136\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
"------------------------------------------------------------\n",
"• Node type: element\n",
" - Number of nodes: 118\n",
" - Number of features: 99\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\element\n",
"------------------------------------------------------------\n",
"• Node type: chemenv\n",
" - Number of nodes: 67\n",
" - Number of features: 15\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\chemenv\n",
"------------------------------------------------------------\n",
"• Node type: crystal_system\n",
" - Number of nodes: 7\n",
" - Number of features: 2\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\crystal_system\n",
"------------------------------------------------------------\n",
"• Node type: magnetic_state\n",
" - Number of nodes: 5\n",
" - Number of features: 2\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\magnetic_state\n",
"------------------------------------------------------------\n",
"• Node type: oxidation_state\n",
" - Number of nodes: 19\n",
" - Number of features: 3\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\oxidation_state\n",
"------------------------------------------------------------\n",
"• Node type: space_group\n",
" - Number of nodes: 230\n",
" - Number of features: 2\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\space_group\n",
"------------------------------------------------------------\n",
"• Node type: wyckoff\n",
" - Number of nodes: 1380\n",
" - Number of features: 2\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\wyckoff\n",
"------------------------------------------------------------\n",
"• Node type: material_site\n",
" - Number of nodes: 2545026\n",
" - Number of features: 15\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material_site\n",
"------------------------------------------------------------\n",
"• Node type: material_lattice\n",
" - Number of nodes: 80643\n",
" - Number of features: 12\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material_lattice\n",
"------------------------------------------------------------\n",
"\n",
"############################################################\n",
"EDGE DETAILS\n",
"############################################################\n",
"Total edge types: 10\n",
"------------------------------------------------------------\n",
"• Edge type: element_element_neighborsByGroupPeriod\n",
" - Number of edges: 391\n",
" - Number of features: 14\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\element_element_neighborsByGroupPeriod\n",
"------------------------------------------------------------\n",
"• Edge type: element_oxiState_canOccur\n",
" - Number of edges: 162\n",
" - Number of features: 8\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\element_oxiState_canOccur\n",
"------------------------------------------------------------\n",
"• Edge type: material_chemenv_containsSite\n",
" - Number of edges: 2542897\n",
" - Number of features: 8\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\material_chemenv_containsSite\n",
"------------------------------------------------------------\n",
"• Edge type: material_crystalSystem_has\n",
" - Number of edges: 80643\n",
" - Number of features: 10\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\material_crystalSystem_has\n",
"------------------------------------------------------------\n",
"• Edge type: material_element_has\n",
" - Number of edges: 270902\n",
" - Number of features: 8\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\material_element_has\n",
"------------------------------------------------------------\n",
"• Edge type: material_lattice_has\n",
" - Number of edges: 80643\n",
" - Number of features: 8\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\material_lattice_has\n",
"------------------------------------------------------------\n",
"• Edge type: material_spg_has\n",
" - Number of edges: 80643\n",
" - Number of features: 10\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\material_spg_has\n",
"------------------------------------------------------------\n",
"• Edge type: element_chemenv_canOccur\n",
" - Number of edges: 270474\n",
" - Number of features: 7\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\element_chemenv_canOccur\n",
"------------------------------------------------------------\n",
"• Edge type: spg_crystalSystem_isApart\n",
" - Number of edges: 230\n",
" - Number of features: 7\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\spg_crystalSystem_isApart\n",
"------------------------------------------------------------\n",
"• Edge type: element_element_bonds\n",
" - Number of edges: 3069943\n",
" - Number of features: 7\n",
" - db_path: ..\\..\\data\\examples\\01\\MatGraphDB\\edges\\element_element_bonds\n",
"------------------------------------------------------------\n",
"\n",
"############################################################\n",
"NODE GENERATOR DETAILS\n",
"############################################################\n",
"Total node generators: 9\n",
"------------------------------------------------------------\n",
"• Generator: element\n",
"Generator Args:\n",
" - generator_func: [<function element at 0x000001E1A2C82C10>]\n",
" - generator_kwargs.base_file: ['C:\\\\Users\\\\lllang\\\\Desktop\\\\Current_Projects\\\\MatGraphDB\\\\matgraphdb\\\\utils\\\\chem_utils\\\\resources\\\\imputed_periodic_table_values.parquet']\n",
" - generator_name: ['element']\n",
" - id: [0]\n",
"Generator Kwargs:\n",
" - base_file: ['C:\\\\Users\\\\lllang\\\\Desktop\\\\Current_Projects\\\\MatGraphDB\\\\matgraphdb\\\\utils\\\\chem_utils\\\\resources\\\\imputed_periodic_table_values.parquet']\n",
"------------------------------------------------------------\n",
"• Generator: chemenv\n",
"Generator Args:\n",
" - generator_func: [<function chemenv at 0x000001E1A2C82D30>]\n",
" - generator_kwargs.base_file: ['C:\\\\Users\\\\lllang\\\\Desktop\\\\Current_Projects\\\\MatGraphDB\\\\matgraphdb\\\\utils\\\\chem_utils\\\\resources\\\\coordination_geometries.parquet']\n",
" - generator_name: ['chemenv']\n",
" - id: [1]\n",
"Generator Kwargs:\n",
" - base_file: ['C:\\\\Users\\\\lllang\\\\Desktop\\\\Current_Projects\\\\MatGraphDB\\\\matgraphdb\\\\utils\\\\chem_utils\\\\resources\\\\coordination_geometries.parquet']\n",
"------------------------------------------------------------\n",
"• Generator: crystal_system\n",
"Generator Args:\n",
" - generator_func: [<function crystal_system at 0x000001E1A2C82E50>]\n",
" - generator_name: ['crystal_system']\n",
" - id: [2]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: magnetic_state\n",
"Generator Args:\n",
" - generator_func: [<function magnetic_state at 0x000001E1A2C82F70>]\n",
" - generator_name: ['magnetic_state']\n",
" - id: [3]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: oxidation_state\n",
"Generator Args:\n",
" - generator_func: [<function oxidation_state at 0x000001E1A2C8D0D0>]\n",
" - generator_name: ['oxidation_state']\n",
" - id: [4]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: space_group\n",
"Generator Args:\n",
" - generator_func: [<function space_group at 0x000001E1A2C8D1F0>]\n",
" - generator_name: ['space_group']\n",
" - id: [5]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: wyckoff\n",
"Generator Args:\n",
" - generator_func: [<function wyckoff at 0x000001E1A2C8D310>]\n",
" - generator_name: ['wyckoff']\n",
" - id: [6]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: material_site\n",
"Generator Args:\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
" - generator_func: [<function material_site at 0x000001E1C487D940>]\n",
" - generator_name: ['material_site']\n",
" - id: [7]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: material_lattice\n",
"Generator Args:\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
" - generator_func: [<function material_lattice at 0x000001E1C487D820>]\n",
" - generator_name: ['material_lattice']\n",
" - id: [8]\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"\n",
"############################################################\n",
"EDGE GENERATOR DETAILS\n",
"############################################################\n",
"Total edge generators: 10\n",
"------------------------------------------------------------\n",
"• Generator: element_oxiState_canOccur\n",
"Generator Args:\n",
" - element_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\element\n",
" - oxiState_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\oxidation_state\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: material_chemenv_containsSite\n",
"Generator Args:\n",
" - chemenv_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\chemenv\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: material_crystalSystem_has\n",
"Generator Args:\n",
" - crystal_system_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\crystal_system\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: element_element_neighborsByGroupPeriod\n",
"Generator Args:\n",
" - element_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\element\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: material_element_has\n",
"Generator Args:\n",
" - element_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\element\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: material_lattice_has\n",
"Generator Args:\n",
" - lattice_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material_lattice\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: material_spg_has\n",
"Generator Args:\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
" - spg_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\space_group\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: element_chemenv_canOccur\n",
"Generator Args:\n",
" - chemenv_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\chemenv\n",
" - element_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\element\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: spg_crystalSystem_isApart\n",
"Generator Args:\n",
" - crystal_system_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\crystal_system\n",
" - spg_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\space_group\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"• Generator: element_element_bonds\n",
"Generator Args:\n",
" - element_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\element\n",
" - material_store: ..\\..\\data\\examples\\01\\MatGraphDB\\nodes\\material\n",
"Generator Kwargs:\n",
"------------------------------------------------------------\n",
"\n"
]
}
],
"source": [
"print(mdb)"
]
}
],
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"display_name": "matgraphdb_dev",
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"name": "python3"
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"name": "ipython",
"version": 3
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"file_extension": ".py",
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