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Graph ID

A universal identifier system for atomistic structures

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What is Graph ID?

Graph ID generates unique, deterministic identifiers for atomistic structures including crystals and molecules. It works by converting atomic structures into graph representations and computing hash-based identifiers that capture both topology and composition.

Quick Example

from pymatgen.core import Structure, Lattice
from graph_id import GraphIDMaker

# Create a structure (NaCl)
structure = Structure.from_spacegroup(
    "Fm-3m",
    Lattice.cubic(5.692),
    ["Na", "Cl"],
    [[0, 0, 0], [0.5, 0.5, 0.5]]
)

# Generate Graph ID
maker = GraphIDMaker()
graph_id = maker.get_id(structure)
print(graph_id)  # Output: NaCl-88c8e156db1b0fd9

How It Works

Graph ID operates through a multi-step process:

flowchart LR
    A[Atomic Structure] --> B[Graph Representation]
    B --> C[Local Environment Analysis]
    C --> D[Compositional Sequences]
    D --> E[Hash-based ID]
  1. Graph Construction: Convert atomic structures into graph representations where atoms are nodes and bonds are edges
  2. Environment Analysis: Analyze the local chemical environment around each atom using compositional sequences
  3. Hash Generation: Compute a deterministic hash-based identifier that captures both topology and composition

Applications

Graph ID is particularly useful for:

  • Materials Databases: Efficient indexing and deduplication of structure databases
  • High-throughput Screening: Rapid identification of unique structures in computational workflows
  • Polymorph Identification: Distinguishing between different polymorphs of the same composition
  • Machine Learning: Feature engineering for materials property prediction

Web Service

Try it online

You can search materials using Graph ID at matfinder.net

Next Steps