def octane(): # CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH3 # with Path("tests/molecules/octane.xyz") as path: structure = Atoms.from_ase_atoms(ase.io.read(path)) structure.cell = 60 * np.identity(3) structure.translate((30., 30., 30.)) yield structure
def hkust1_3x3x3_xyz(): with Path("tests/hkust-1/hkust-1-3x3x3.xyz") as path: structure = Atoms.from_ase_atoms(ase.io.read(path)) structure.cell = 79.0290 * np.identity(3) yield structure
def benzene(): with Path("tests/molecules/benzene.xyz") as path: yield Atoms.from_ase_atoms(ase.io.read(path))
""" Run and visualize with: python -m cProfile -o hkustperf.pstats -s tottime hkustperf.py snakeviz hkustperf.pstats """ import ase import ase.io import numpy as np from mofun import find_pattern_in_structure, replace_pattern_in_structure, Atoms hkust1_cif = Atoms.load_cif("../tests/hkust-1/hkust-1-with-bonds.cif") benzene = Atoms.from_ase_atoms(ase.io.read("../tests/molecules/benzene.xyz")) hkust1_repped = hkust1_cif.replicate(repldims=(3, 3, 3)) match_indices = find_pattern_in_structure(hkust1_repped, benzene)