matgraphdb 0.3.0

Welcome to MatGraphDB, a powerful Python package designed to interface with primary and graph databases for advanced material analysis.

MatGraphDB

Table of Contents

• Introduction to MatGraphDB
• Installing
• Usage
  • Interacting with the materials database
  • Interacting with the graph database
• Contributing
• License

Introduction to MatGraphDB

To be written..

Installing

Installing via pip

pip install matgraphdb

Installing from github

git clone https://github.com/lllangWV/MatGraphDB.git
cd MatGraphDB
pip install -e .

Usage

Interacting with the materials database.

Initialize MatGraphDB

from matgraphdb import MatGraphDB

# Initialize MatGraphDB
mgdb = MatGraphDB(storage_path="MatGraphDB")
print(mgdb.summary())

Adding material properties

You can add any material to the database by either providing a structure or coords, species, and lattice, then using the create_material or create_materials function.

Any material add to the database gets indexed. This is stored in the id column.

from pymatgen.core import Structure

# Add material to the database
material_data_1 = {
    "structure": structure,
    "properties": {
        "material_id": "mp-1",
        "source": "example",
        "thermal_conductivity": {"value": 2.5, "unit": "W/mK"},
    },
}

# or by coords, species, lattice
material_data_2 = {
    "coords":  [[0, 0, 0], [0.5, 0.5, 0.5]],
    "species": ["Mg", "O"],
    "lattice": [[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],
    "properties": {
        "material_id": "mp-2",
        "source": "example_manual",
        "band_gap": {"value": 1.2, "unit": "eV"},
    },
}

result = mgdb.create_material(
    coords=material_data_2["coords"],
    species=material_data_2["species"],
    lattice=material_data_2["lattice"],
    properties=material_data_2["properties"],
)
# Add material by structure
db.create_material(
                structure=material_data_1["structure"],
                properties=material_data_1["properties"])


materials=[material_data_1,material_data_2]

# Add multiple materials
mgdb.create_materials(materials)

Reading Materials

To read materials from the database, you can use the read_materials function. This function takes in a columns parameter, which specifies the columns to read from the database. The filters parameter specifies the filters to apply to the database. This will only read the matched materials to memory.

materials = mgdb.read_materials( 
    columns=["material_id", "elements", "band_gap.value"],
    filters=[pc.field("band_gap.value") == 1.2]
    )

Updating Materials

To update materials in the database, you can use the update_materials function. For updates you must provide the id of the material you want to update. You can also provide the update_keys parameter to specify the columns to update on as well, this is usefull if you import an existing dataset from another database.

update_data = [
    {
        "id": 0,
        "band_gap": {"value": 3.6, "unit": "eV"},
    },
]

materials = mgdb.update_materials(update_data)


update_data = [
    {
        "material_id": "mp-1",
        "band_gap": {"value": 3.6, "unit": "eV"},
    },
]
materials = mgdb.update_materials(update_data, update_keys=["material_id"])

Deleting Materials

To delete materials from the database, you can use the delete_materials function. You can provide a list of ids to delete.

materials = mgdb.delete_materials(ids=[0])

Interacting with the graph database

Contributing

Contributions are welcome! Please open an issue or submit a pull request on GitHub.

License

This project is licensed under the MIT License. See the LICENSE file for details.

Authors

Logan Lang, Aldo Romero, Eduardo Hernandez,

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Note: This project is in its initial stages. Features and APIs are subject to change. Please refer to the latest documentation and release notes for updates.