def test_replace_pattern_in_structure__replace_hydrogens_in_octane_with_nothing(octane): # CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH3 # search_pattern = Atoms(elements='H', positions=[(0, 0, 0)]) replace_pattern = Atoms() final_structure = replace_pattern_in_structure(octane, search_pattern, replace_pattern) assert list(final_structure.elements) == ["C"] * 8
def test_replace_pattern_in_structure__replacement_pattern_across_pbc_gets_coordinates_within_unit_cell(): structure = Atoms(elements='CNNF', positions=[(9.1, 0., 0), (0.1, 0., 0), (1.1, 0., 0.), (2.1, 0., 0.)], cell=10*np.identity(3)) search_pattern = Atoms(elements='CN', positions=[(0., 0., 0), (1.0, 0., 0.)]) replace_pattern = search_pattern final_structure = replace_pattern_in_structure(structure, search_pattern, replace_pattern) assert Counter(final_structure.elements) == Counter(structure.elements) assert_structure_positions_are_unchanged(structure, final_structure)
def test_replace_pattern_in_structure__replace_hydrogens_in_octane_with_fluorines_half_the_time(octane): search_pattern = Atoms(elements='H', positions=[(0, 0, 0)]) replace_pattern = Atoms(elements='F', positions=[(0, 0, 0)]) match_indices = find_pattern_in_structure(octane, search_pattern) final_structure = replace_pattern_in_structure(octane, search_pattern, replace_pattern, replace_fraction=0.5) assert Counter(final_structure.elements) == {"H":9, "F": 9, "C": 8} assert_structure_positions_are_unchanged(octane, final_structure)
def test_replace_pattern_in_structure__overlapping_match_patterns_errors(): structure = Atoms(elements='CNNC', positions=[(0., 0., 0), (1.0, 0., 0.), (2.0, 0., 0.), (3.0, 0., 0.)], cell=100*np.identity(3)) search_pattern = Atoms(elements='NNC', positions=[(0., 0., 0), (1.0, 0., 0.), (2.0, 0., 0.)]) replace_pattern = Atoms(elements='FFC', positions=[(0., 0., 0), (1.0, 0., 0.), (2.0, 0., 0.)]) with pytest.raises(AtomsShouldNotBeDeletedTwice): final_structure = replace_pattern_in_structure(structure, search_pattern, replace_pattern)
def test_replace_pattern_in_structure__replace_CH3_in_octane_with_CH3(octane): search_pattern = Atoms(elements='CHHH', positions=[(0, 0, 0), (-0.538, -0.635, 0.672), (-0.397, 0.993, 0.052), (-0.099, -0.371, -0.998)]) replace_pattern = Atoms(elements='CHHH', positions=search_pattern.positions) final_structure = replace_pattern_in_structure(octane, search_pattern, replace_pattern) assert Counter(final_structure.elements) == {"C": 8, "H": 18} # note the positions are not EXACTLY the same because the original structure has slightly # different coordinates for the two CH3 groups! assert_structure_positions_are_unchanged(octane, final_structure, max_delta=0.1)
def test_replace_pattern_in_structure__two_points_on_x_axis_positions_are_unchanged(): structure = Atoms(elements='CNNC', positions=[(0., 0., 0), (1.0, 0., 0.), (2.0, 0., 0.), (3.0, 0., 0.)], cell=100*np.identity(3)) search_pattern = Atoms(elements='NN', positions=[(0.0, 0., 0), (1.0, 0., 0.)]) replace_pattern = Atoms(elements='FF', positions=[(0., 0., 0), (1.0, 0., 0.)]) final_structure = replace_pattern_in_structure(structure, search_pattern, replace_pattern) assert Counter(final_structure.elements) == {"C":2, "F": 2} assert_structure_positions_are_unchanged(structure, final_structure)
def test_replace_pattern_in_structure__replace_no_bonds_linker_with_linker_with_bonds_angles_has_bonds_angles(uio66_linker_no_bonds, uio66_linker_some_bonds): structure = uio66_linker_no_bonds.copy() structure.cell = 100*np.identity(3) final_structure = replace_pattern_in_structure(structure, uio66_linker_no_bonds, uio66_linker_some_bonds, axis1a_idx=0, axis1b_idx=15) assert Counter(final_structure.elements) == {'C': 8, 'O': 4, 'H': 4} assert_structure_positions_are_unchanged(structure, final_structure, max_delta=0.1) assert_topo(final_structure.dihedrals, uio66_linker_some_bonds.dihedrals, final_structure.dihedral_types, uio66_linker_some_bonds.dihedral_types, final_structure.dihedral_type_coeffs, uio66_linker_some_bonds.dihedral_type_coeffs)
def test_replace_pattern_in_structure__special2_rotated_pattern_replaced_with_itself_does_not_change_positions(): search_pattern = Atoms(elements='CCH', positions=[(0., 0., 0.), (4., 0., 0.),(0., 1., 0.)]) replace_pattern = Atoms(elements='FFHe', positions=search_pattern.positions) structure = search_pattern.copy() structure.cell = 15 * np.identity(3) r = R.from_quat([ 0.02814096, 0.99766676, 0.03984918, -0.04776152]) structure.positions = r.apply(structure.positions) structure.positions = structure.positions % 15 final_structure = replace_pattern_in_structure(structure, search_pattern, replace_pattern, axis1a_idx=0, axis1b_idx=1) assert_structure_positions_are_unchanged(structure, final_structure)
def test_replace_pattern_in_structure__in_uio66_replacing_linker_with_linker_does_not_change_positions(): with Path("tests/uio66/uio66.cif") as path: structure = Atoms.load_cif(path) with Path("tests/uio66/uio66-linker.cif") as path: search_pattern = Atoms.load_cif(path) with Path("tests/uio66/uio66-linker-fluorinated.cif") as path: replace_pattern = Atoms.load_cif(path) final_structure = replace_pattern_in_structure(structure, search_pattern, replace_pattern) assert Counter(final_structure.elements) == {'C': 192, 'O': 120, 'F': 96, 'Zr': 24}
def test_replace_pattern_in_structure__pattern_and_reverse_pattern_on_x_axis_positions_are_unchanged(): structure = Atoms(elements='HHCCCHH', positions=[(-1., 1, 0), (-1., -1, 0), (0., 0., 0), (1., 0., 0.), (3., 0., 0.), (4., 1, 0), (4., -1, 0)], cell=7*np.identity(3)) structure.translate([2, 2, 0.1]) search_pattern = Atoms(elements='HHC', positions=[(0., 1, 0), (0., -1, 0), (1., 0., 0.)]) replace_pattern = Atoms(elements='HHC', positions=[(0., 1, 0), (0., -1, 0), (1., 0., 0.)]) final_structure = replace_pattern_in_structure(structure, search_pattern, replace_pattern) assert Counter(final_structure.elements) == {"C":3, "H": 4} assert_structure_positions_are_unchanged(structure, final_structure)
def test_replace_pattern_in_structure__special_rotated_pattern_replaced_with_itself_does_not_change_positions(): search_pattern = Atoms(elements='CCH', positions=[(0., 0., 0.), (4., 0., 0.),(0., 1., 0.)]) replace_pattern = Atoms(elements='FFHe', positions=search_pattern.positions) structure = search_pattern.copy() structure.cell = [15] * np.identity(3) r = R.from_quat([-0.4480244, -0.50992783, 0.03212454, -0.7336319 ]) structure.positions = r.apply(structure.positions) structure.positions = structure.positions % 15 final_structure = replace_pattern_in_structure(structure, search_pattern, replace_pattern, axis1a_idx=0, axis1b_idx=1) assert_structure_positions_are_unchanged(structure, final_structure)
def test_replace_pattern_in_structure__3way_symmetrical_structure_raises_position_exception(): structure = Atoms(elements='CCHH', positions=[(0., 0., 0.), (1., 0., 0.),(0., 1., 0.), (0., 0., 1.)]) structure.translate((3,3,3)) structure.cell = 15 * np.identity(3) search_pattern = structure.copy() replace_pattern = Atoms(elements='FFHeHe', positions=search_pattern.positions) with pytest.raises(PositionsNotEquivalent): final_structure = replace_pattern_in_structure(structure, search_pattern, replace_pattern, verbose=True)
def test_replace_pattern_in_structure__three_points_on_x_axis_positions_are_unchanged(): # this test exists to verify that for a search pattern with more than 2 atoms where all atoms lie on the same axis # there are no errors, since there is an extra unnecessary quaternion calcuation to orient the replacement pattern # into the final position structure = Atoms(elements='CNNNC', positions=[(0., 0., 0), (1., 0., 0.), (2., 0., 0.), (3., 0., 0.), (4., 0., 0.)], cell=100*np.identity(3)) search_pattern = Atoms(elements='NNN', positions=[(0., 0., 0), (1.0, 0., 0.), (2.0, 0., 0.)]) replace_pattern = Atoms(elements='FFF', positions=[(0., 0., 0), (1.0, 0., 0.), (2.0, 0., 0.)]) final_structure = replace_pattern_in_structure(structure, search_pattern, replace_pattern) assert Counter(final_structure.elements) == {"C":2, "F": 3} assert_structure_positions_are_unchanged(structure, final_structure)
def test_replace_pattern_in_structure__100_randomly_rotated_patterns_replaced_with_itself_does_not_change_positions(): search_pattern = Atoms(elements='CCH', positions=[(0., 0., 0.), (4., 0., 0.),(0., 1., 0.)]) replace_pattern = Atoms(elements='FFHe', positions=search_pattern.positions) structure = search_pattern.copy() structure.cell = 15 * np.identity(3) for _ in range(100): r = R.random(1) print("quat: ", r.as_quat()) structure.positions = r.apply(structure.positions) dp = np.random.random(3) * 15 print(dp) structure.translate(dp) structure.positions = structure.positions % 15 final_structure = replace_pattern_in_structure(structure, search_pattern, replace_pattern, axis1a_idx=0, axis1b_idx=1) assert_structure_positions_are_unchanged(structure, final_structure)
def functionalize_structure_with_linkers(structure_path, linker_path, fnlinkers, output_dir=Path()): linker = Atoms.from_cml(Path(linker_path)) structure = Atoms.from_cif(structure_path) output_dir = Path(output_dir) assign_pair_params_to_structure(structure) for fnlinker_path in fnlinkers: print("reading %s" % fnlinker_path) fnlinker = Atoms.from_lammps_data(open(fnlinker_path, "r"), use_comment_for_type_labels=True) try: new_structure = replace_pattern_in_structure( structure, linker, fnlinker) with open( output_dir.joinpath(Path(fnlinker_path).stem + ".lmpdat"), "w") as fd: new_structure.to_lammps_data(fd) except Exception as e: print("ERROR! ", e.args)
def test_replace_pattern_in_structure__in_hkust1_offset_replacing_benzene_with_benzene_does_not_change_positions(hkust1_cif, benzene): hkust1_cif.translate((-4,-4,-4)) hkust1_cif.positions = hkust1_cif.positions % np.diag(hkust1_cif.cell) final_structure = replace_pattern_in_structure(hkust1_cif, benzene, benzene, axis1a_idx=0, axis1b_idx=7) assert Counter(final_structure.elements) == Counter(hkust1_cif.elements) assert_structure_positions_are_unchanged(hkust1_cif, final_structure, max_delta=0.1)
def test_replace_pattern_in_structure__in_hkust1_replacing_benzene_with_benzene_does_not_change_positions(hkust1_cif, benzene): final_structure = replace_pattern_in_structure(hkust1_cif, benzene, benzene, axis1a_idx=0, axis1b_idx=7) assert Counter(final_structure.elements) == Counter(hkust1_cif.elements) assert_structure_positions_are_unchanged(hkust1_cif, final_structure, max_delta=0.1)
for repldims in all_repldims: structure = uio67.replicate(repldims=repldims) time_s = time.process_time() perf_s = time.perf_counter() patterns = find_pattern_in_structure(structure, uio67_linker) output_csv.writerow( ("uio67", "%dx%dx%dx" % repldims, len(structure), len(patterns), 24 * repldims[0] * repldims[1] * repldims[2], time.process_time() - time_s, time.perf_counter() - perf_s)) for repldims in all_repldims: structure = uio66.replicate(repldims=repldims) time_s = time.process_time() perf_s = time.perf_counter() patterns = replace_pattern_in_structure(structure, uio66_linker, uio66_linker) output_csv.writerow( ("uio66", "%dx%dx%dx" % repldims, len(structure), len(patterns), time.process_time() - time_s, time.perf_counter() - perf_s)) for repldims in all_repldims: structure = uio67.replicate(repldims=repldims) time_s = time.process_time() perf_s = time.perf_counter() patterns = replace_pattern_in_structure(structure, uio67_linker, uio67_linker) output_csv.writerow( ("uio67", "%dx%dx%dx" % repldims, len(structure), len(patterns), time.process_time() - time_s, time.perf_counter() - perf_s))
def mofun_cli(inputpath, outputpath, find_path=None, replace_path=None, replace_fraction=1.0, axis1a_idx=0, axis1b_idx=-1, axis2_idx=None, dumppath=None, chargefile=None, replicate=None, mic=None, framework_element=None, pp=False): atoms = Atoms.load(inputpath) # upate positions from lammps dump file if dumppath is not None: # update positions in original atoms file with new positions dumpatoms = ase.io.read(dumppath, format="lammps-dump-text") assert len(dumpatoms.positions) == len(atoms.positions) atoms.positions = dumpatoms.positions # update charges if chargefile is not None: charges = np.array( [float(line.strip()) for line in chargefile if line.strip() != '']) assert len(charges) == len(atoms.positions) atoms.charges = charges if replicate is not None: atoms = atoms.replicate(replicate) # replicate to meet minimum image convention, if necessary if mic is not None: repls = np.array(np.ceil(2 * mic / np.diag(atoms.cell)), dtype=int) atoms = atoms.replicate(repls) if pp: assign_pair_params_to_structure(atoms) if replace_path is not None and find_path is None: print("Cannot perform a replace operation without a find operation") elif find_path is not None: search_pattern = Atoms.load(find_path) if replace_path is not None: replace_pattern = Atoms.load(replace_path) atoms = replace_pattern_in_structure( atoms, search_pattern, replace_pattern, axis1a_idx=axis1a_idx, axis1b_idx=axis1b_idx, axis2_idx=axis2_idx, replace_fraction=replace_fraction) else: results = find_pattern_in_structure(atoms, search_pattern) print("Found %d instances of the search_pattern in the structure" % len(results)) print(results) # set framework elements to specified element-only works on ASE exports if framework_element is not None: atoms.symbols[atoms.atom_groups == 0] = framework_element if outputpath.suffix in ['.lmpdat', '.mol']: atoms.save(outputpath) else: print("INFO: Trying output using ASE") aseatoms = atoms.to_ase() if framework_element is not None: aseatoms.symbols[atoms.atom_groups == 0] = framework_element aseatoms.set_pbc(True) aseatoms.write(outputpath)
def test_replace_pattern_in_structure__replace_hydrogens_in_octane_with_nothing_quarter_time(octane): search_pattern = Atoms(elements='H', positions=[(0, 0, 0)]) final_structure = replace_pattern_in_structure(octane, search_pattern, Atoms(), replace_fraction=0.25) assert Counter(final_structure.elements) == {"H": 14, "C": 8}
def test_replace_pattern_in_structure__replace_hydrogens_in_octane_with_hydrogens(octane): search_pattern = Atoms(elements='H', positions=[(0, 0, 0)]) replace_pattern = search_pattern final_structure = replace_pattern_in_structure(octane, search_pattern, replace_pattern) assert Counter(final_structure.elements) == {"H": 18, "C": 8} assert_structure_positions_are_unchanged(octane, final_structure)