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)