Materials Science Guide

This guide covers the fragmentation of materials science systems, including surfaces and other periodic systems.

Prerequisites

from autofragment import ChemicalSystem
from autofragment.partitioners import SurfacePartitioner
from autofragment.io.readers import read_cif, read_poscar

Loading Periodic Systems

From CIF Files

system = read_cif("structure.cif")
print(f"Atoms: {system.n_atoms}")
if system.lattice:
    print(f"Lattice: {system.lattice}")

From VASP Files

system = read_poscar("POSCAR")

Lattice Operations

lattice = system.lattice
print(f"a, b, c: {lattice.lengths}")
print(f"alpha, beta, gamma: {lattice.angles}")
print(f"Volume: {lattice.volume:.2f} A^3")

Surface Systems

partitioner = SurfacePartitioner(
    surface_normal=2,         # z-axis
    n_surface_layers=2,
    n_bulk_layers=3,
)
fragments = partitioner.partition(slab)

Future Work

The following partitioners are planned for future releases but not yet implemented:

MOFPartitioner: Metal-Organic Framework decomposition into nodes and linkers
ZeolitePartitioner: Aluminosilicate framework partitioning

Similarly, the following writers are planned:

VASP writer: POSCAR output for periodic fragments
Quantum ESPRESSO writer: pw.in output for periodic DFT

Tips

Use large enough supercells to avoid periodic image artifacts
Keep complete coordination spheres in fragments
Protect aromatic rings and functional groups
Use appropriate charges for accurate embedding