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Examples

This section provides practical examples of using Graph ID in various scenarios.

Available Examples

  • Machine Learning

    Use Graph ID features for materials property prediction

    Machine Learning

Quick Examples

Deduplicating a CIF Collection

from pathlib import Path
from pymatgen.core import Structure
from graph_id import GraphIDMaker

maker = GraphIDMaker()
seen_ids = {}

for cif_file in Path("structures/").glob("*.cif"):
    structure = Structure.from_file(cif_file)
    graph_id = maker.get_id(structure)

    if graph_id not in seen_ids:
        seen_ids[graph_id] = cif_file
        print(f"New: {cif_file.name} -> {graph_id}")
    else:
        print(f"Duplicate: {cif_file.name} matches {seen_ids[graph_id].name}")

Finding Isostructural Materials

from graph_id_cpp import GraphIDGenerator

# Topology-only mode ignores element types
topo_gen = GraphIDGenerator(topology_only=True)

structures = load_structures()  # Your loading function

# Group by topology
topology_groups = {}
for name, struct in structures.items():
    topo_id = topo_gen.get_id(struct)
    if topo_id not in topology_groups:
        topology_groups[topo_id] = []
    topology_groups[topo_id].append(name)

# Print groups with multiple members
for topo_id, members in topology_groups.items():
    if len(members) > 1:
        print(f"Isostructural group ({topo_id[:8]}...): {members}")

Comparing Database Entries

from graph_id import GraphIDMaker
from graph_id_db import Finder

maker = GraphIDMaker()
finder = Finder()

# Your structure
my_structure = Structure.from_file("my_material.cif")
my_id = maker.get_id(my_structure)

# Search database
matches = finder.find(my_id)

if matches:
    print(f"Found in Materials Project: {matches}")
else:
    print("Novel structure - not in database!")

Jupyter Notebooks

The repository includes Jupyter notebook examples:

Test Files

The test suite in tests/ provides additional usage examples:

  • tests/cpp/test_graph_id.py - Basic functionality tests
  • tests/cpp/test_near_neighbor.py - Neighbor detection tests
  • tests/cpp/test_maker.py - GraphIDMaker tests