def test_find_match2(self): sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5, primitive_cell=True, scale=True, attempt_supercell=False) l = Lattice.orthorhombic(1, 2, 3) s1 = Structure(l, ['Si', 'Si'], [[0, 0, 0.1], [0, 0, 0.2]]) s2 = Structure(l, ['Si', 'Si'], [[0, 0.1, 0], [0, 0.1, -0.95]]) s1, s2, fu, s1_supercell = sm._preprocess(s1, s2, False) match = sm._strict_match(s1, s2, fu, s1_supercell=False, use_rms=True, break_on_match=False) scale_matrix = match[2] s2.make_supercell(scale_matrix) s2.translate_sites(range(len(s2)), match[3]) self.assertAlmostEqual(np.sum(s2.frac_coords), 0.3) self.assertAlmostEqual(np.sum(s2.frac_coords[:, :2]), 0)
def test_find_match1(self): sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5, primitive_cell=True, scale=True, attempt_supercell=False) l = Lattice.orthorhombic(1, 2, 3) s1 = Structure(l, ['Si', 'Si', 'Ag'], [[0, 0, 0.1], [0, 0, 0.2], [.7, .4, .5]]) s2 = Structure(l, ['Si', 'Si', 'Ag'], [[0, 0.1, 0], [0, 0.1, -0.95], [.7, .5, .375]]) s1, s2, fu, s1_supercell = sm._preprocess(s1, s2, False) match = sm._strict_match(s1, s2, fu, s1_supercell=True, use_rms=True, break_on_match=False) scale_matrix = match[2] s2.make_supercell(scale_matrix) fc = s2.frac_coords + match[3] fc -= np.round(fc) self.assertAlmostEqual(np.sum(fc), 0.9) self.assertAlmostEqual(np.sum(fc[:, :2]), 0.1) cart_dist = np.sum(match[1] * (l.volume / 3)**(1 / 3)) self.assertAlmostEqual(cart_dist, 0.15)
def test_find_match2(self): sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5, primitive_cell=True, scale=True, attempt_supercell=False) l = Lattice.orthorhombic(1, 2, 3) s1 = Structure(l, ["Si", "Si"], [[0, 0, 0.1], [0, 0, 0.2]]) s2 = Structure(l, ["Si", "Si"], [[0, 0.1, 0], [0, 0.1, -0.95]]) s1, s2, fu, s1_supercell = sm._preprocess(s1, s2, False) match = sm._strict_match(s1, s2, fu, s1_supercell=False, use_rms=True, break_on_match=False) scale_matrix = match[2] s2.make_supercell(scale_matrix) s2.translate_sites(range(len(s2)), match[3]) self.assertAlmostEqual(np.sum(s2.frac_coords), 0.3) self.assertAlmostEqual(np.sum(s2.frac_coords[:, :2]), 0)
def test_find_match1(self): sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5, primitive_cell=True, scale=True, attempt_supercell=False) l = Lattice.orthorhombic(1, 2, 3) s1 = Structure(l, ["Si", "Si", "Ag"], [[0, 0, 0.1], [0, 0, 0.2], [0.7, 0.4, 0.5]]) s2 = Structure(l, ["Si", "Si", "Ag"], [[0, 0.1, 0], [0, 0.1, -0.95], [0.7, 0.5, 0.375]]) s1, s2, fu, s1_supercell = sm._preprocess(s1, s2, False) match = sm._strict_match(s1, s2, fu, s1_supercell=True, use_rms=True, break_on_match=False) scale_matrix = match[2] s2.make_supercell(scale_matrix) fc = s2.frac_coords + match[3] fc -= np.round(fc) self.assertAlmostEqual(np.sum(fc), 0.9) self.assertAlmostEqual(np.sum(fc[:, :2]), 0.1) cart_dist = np.sum(match[1] * (l.volume / 3) ** (1 / 3)) self.assertAlmostEqual(cart_dist, 0.15)