コード例 #1
0
ファイル: mc_run16.py プロジェクト: hackberie/00_workSpace
def prepare(conc, size, temp):
    path = "."
    unitcell = UnitCell.from_file("log.txt")
    ecis = Ecis.from_dirc(".")
    matrix = Matrix(conc, unitcell, ecis, size)
    matrix.adjust_conc_fine(conc)
    mc = MonteCarlo(matrix, temp)
    return mc
コード例 #2
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    def _test_montecalro(self):
        """ montecalro """
        path = os.path.join(self.PATH, "MonteCarlo", "FeH_BCCI")
        unitcell = UnitCell.from_file(os.path.join(path, "log.txt"))
        conc = 0.2
        ecis = Ecis.from_dirc(path)
        matrix = Matrix(conc, unitcell, ecis, 20)
        mc = MonteCarlo(matrix, 5000)
        pairs = mc.get_exchange_pairs([1, 3, 5])
        assert pairs[0].sum() == pairs[1].sum()
        assert (matrix.matrix[pairs[0]] == 0).all()
        assert (matrix.matrix[pairs[1]] == 1).all()
        mc.exe_flip(pairs)

        mc.loop_test(1)
コード例 #3
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    def test_SymmetryOperator(self):
        """ SymmetryOperator """
        path = os.path.join(self.PATH, "UnitCell")
        unitcell = UnitCell.from_file(os.path.join(path, "log.txt"))

        # opertate_symm
        ## 160412
        clus = [[1/2, 1/2, 0]]
        clus_dst = SymmetryOperator.operate_symm(clus, unitcell)
        assert np.array(clus_dst).shape == (6, 1, 4)
        clus = [[0, 1/2, 1/2], [3/4, 1/2, 1/4]]
        clus_dst = SymmetryOperator.operate_symm(clus, unitcell)
        assert np.array(clus_dst).shape == (48, 2, 4)
        clus = [[0, 1/2, 1/2], [1/2, 1/2, 0]]
        assert np.array(
            SymmetryOperator.operate_symm(clus, unitcell)).shape == (12, 2, 4)

        # centering
        ## 160412
        clus = [[0, 1/2, 1/2], [1/2, 1/2, 0]]
        out = [[[0.5, 0, -0.5]]]
        assert (np.array(
            SymmetryOperator.centerings(clus, unitcell)[6]) == out).all()
        out = [[[-0.5, 0, 0.5]]]
        assert (np.array(
            SymmetryOperator.centerings(clus, unitcell)[8]) == out).all()
        clus = [[3/4, 1/2, 1/4]]
        assert not SymmetryOperator.centerings(clus, unitcell)[0][0]

        # get_symmetrized_clusters
        ## 160412
        clus = [[1/2, 1/2, 0], [-1/2, -1/2, 0]] # delta = [1, 0, 0]
        out = [[[0, -1, -1, 0]], [[0, 1, 1, 0]]]
        assert SymmetryOperator.get_equiv_clusters(
            clus, unitcell)[6] == out

        clus = [[1/2, 0, 1/2], [3/4, 1/2, 1/4]]
        dst = SymmetryOperator.get_equiv_clusters(clus, unitcell)
        assert set(dst.keys()) == set(range(9))

        # centerings_idx
        ## 160307
        clus = [unitcell.site2idx(site)
                for site in [[0, 1/2, 1/2], [1/2, 1/2, 0]]]
        out = {8: [np.array([[0, 0, 0, -2]])],
               6: [np.array([[0, 0, 0, 2]])]}
        assert (SymmetryOperator.centerings_idx(clus)[8][0] == out[8][0]).all()
        assert (SymmetryOperator.centerings_idx(clus)[6][0] == out[6][0]).all()
コード例 #4
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    def test_UnitCell(self):
        """ UnitCell """
        path = os.path.join(self.PATH, "UnitCell")

        # from_file
        unitcell = UnitCell.from_file(os.path.join(path, "log.txt"))

        # cell
        ## 160305
        out = np.array(
            [[1.414893, 1.414893, 1.414893],
             [1.414893, -1.414893, -1.414893],
             [-1.414893, 1.414893, -1.414893]])
        assert (unitcell.atoms.cell == out).all()

        # site
        ## 160305
        out = np.array(
            [[0.75, 0.50, 0.25],
             [0.75, 0.25, 0.50],
             [0.50, 0.25, 0.75],
             [0.25, 0.75, 0.50],
             [0.50, 0.75, 0.25],
             [0.25, 0.50, 0.75],
             [0.00, 0.50, 0.50],
             [0.50, 1.00, 0.50],
             [0.50, 0.50, 0.00]])
        assert np.allclose(unitcell.atoms.get_scaled_positions(), out)

        # out = ['symmorphic', '48']
        # assert xtal.symm == out
        out = [0, 0, 0, 0, 0, 0, 6, 6, 6]
        assert (unitcell.symm['equivalent_atoms'] == out).all()

        # site2idx
        ## 160305
        site = np.array([-0.75, -0.5, -0.25])
        assert (unitcell.site2idx(site) == [-1, -1, -1, 5])
        site = [1/2, 0, 1/2]
        assert (unitcell.site2idx(site) == [0, -1, 0, 7])
        site = [1, 1/2, 1/2]
        assert (unitcell.site2idx(site) == [1, 0, 0, 6])
        site = np.array([-0.75, -0.5, 0.25])
        try:
            unitcell.site2idx(site)
            assert False
        except KeyError:
            assert True

        # site2pos
        ## 160306
        site = np.array([3/4, 1/2, 1/4])
        out = [1/2, 1/4, 0]
        pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
        assert np.allclose(pos, out)
        site = np.array([3/4, 1/4, 1/2])
        out = [1/4, 1/2, 0]
        pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
        assert np.allclose(pos, out)
        site = np.array([1/2, 1/4, 3/4])
        out = [0, 1/2, -1/4]
        pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
        assert np.allclose(pos, out)
        site = np.array([1/4, 3/4, 1/2])
        out = [1/4, 0, -1/2]
        pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
        assert np.allclose(pos, out)
        site = np.array([1/2, 3/4, 1/4])
        out = [1/2, 0, -1/4]
        pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
        assert np.allclose(pos, out)
        site = np.array([1/4, 1/2, 3/4])
        out = [0, 1/4, -1/2]
        pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
        assert np.allclose(pos, out)

        site = [1/2, 1/2, 0]
        pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
        assert np.allclose(pos, [1/2, 0, 0])
        site = [-1/2, -1/2, 0]
        pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
        assert np.allclose(pos, [-1/2, 0, 0])

        site = np.array([1, 1/2, 1/2])
        pos = unitcell.site2pos(site) / unitcell.atoms.cell[0, 0] / 2
        assert np.allclose(pos, [1/2, 1/2, 0])



        # get_ineq_group
        ## 160305
        assert unitcell.get_ineq_group([-0.75, -0.5, -0.25]) == 0
        assert unitcell.get_ineq_group([1, -0.5, -0.5]) == 6
        assert unitcell.get_ineq_group([3/4, 1/2, 1/4]) == 0
        try:
            unitcell.get_ineq_group([0.0, 1.0, -0.5])
            assert False
        except KeyError:
            assert True
コード例 #5
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    def test_Matrix(self):
        """ Matrix """
        # __init__
        # TO
        ## 160309
        path = os.path.join(self.PATH, "Matrix", "AlCu_TO")
        unitcell = UnitCell.from_file(os.path.join(path, "log.txt"))
        ecis = Ecis.from_dirc(path)
        conc = 0
        matrix = Matrix(conc, unitcell, ecis, 2)
        # FCC (HCP0*A1B0*TO)

        matrix.matrix[:] = 1
        assert np.allclose(matrix.get_energy(), -1.440741)
        # FCC (HCP0*A0B1*TO)
        matrix.matrix[:] = 0
        assert np.allclose(matrix.get_energy(), -115.824971)
        # L10 (HCP3*A1B1)
        matrix.matrix[:] = 0
        matrix.matrix[0, 0, 0, 0] = 1
        matrix.matrix[1, 1, 1, 0] = 1
        matrix.matrix[0, 1, 0, 0] = 1
        matrix.matrix[1, 0, 1, 0] = 1
        assert np.allclose(matrix.get_energy(), -211.482477833)
        # L12 (HCP27*A1B3)
        matrix.matrix[0, 0, 0, 0] = 0
        matrix.matrix[1, 1, 1, 0] = 0
        assert np.allclose(matrix.get_energy(), -173.72808675)
        # L12 (HCP28*A3B1)
        matrix.matrix[:] = 1
        matrix.matrix[0, 1, 0, 0] = 0
        matrix.matrix[1, 0, 1, 0] = 0
        assert np.allclose(matrix.get_energy(), -172.812058)

        # BCCI 2N
        ## 160311
        path = os.path.join(self.PATH, "Matrix", "FeH_BCCI_2N")
        unitcell = UnitCell.from_file(os.path.join(path, "log.txt"))
        conc = 0.5
        ecis = Ecis.from_dirc(path)
        # BCCI (HCP0*A9B0*OP)
        matrix = Matrix(conc, unitcell, ecis, 1,
                        order=[1, 1, 1, 1, 1, 1, 1, 1, 1])
        assert np.allclose(matrix.get_energy(), -17.1659116)

        # FeH6 (HCP99999*A6B3*OP)
        matrix = Matrix(conc, unitcell, ecis, 2,
                        order=[1, 1, 1, 1, 1, 1, 0, 0, 0])
        assert np.allclose(matrix.get_energy(), 0)
        # FeH3 (HCP10*A3B6*OP)
        matrix = Matrix(conc, unitcell, ecis, 3,
                        order=[0, 0, 0, 0, 0, 0, 1, 1, 1])
        assert np.allclose(matrix.get_energy(), 0)

        # FeH5 (HCP99998*5B4*OP)
        matrix = Matrix(conc, unitcell, ecis, 4,
                        order=[1, 0, 1, 0, 1, 0, 1, 0, 1])
        assert np.allclose(matrix.get_energy(), -.572197E+01)
        # FeH6 (HCP99997*A6B3*OP)
        matrix = Matrix(conc, unitcell, ecis, 5,
                        order=[1, 1, 1, 0, 0, 0, 1, 1, 1])
        assert np.allclose(matrix.get_energy(), -.858296E+01)



        # # BCCI
        # ## 160309
        path = os.path.join(self.PATH, "Matrix", "FeH_BCCI")
        unitcell = UnitCell.from_file(os.path.join(path, "log.txt"))
        conc = 0.5
        ecis = Ecis.from_dirc(path)
        # BCCI (HCP0*A9B0*OP)
        matrix = Matrix(conc, unitcell, ecis, 1,
                        order=[1, 1, 1, 1, 1, 1, 1, 1, 1])
        assert np.allclose(matrix.get_energy(), 0.132641E+01)
        # FeH6 (HCP99999*A6B3*OP)
        matrix = Matrix(conc, unitcell, ecis, 2,
                        order=[1, 1, 1, 1, 1, 1, 0, 0, 0])
        assert np.allclose(matrix.get_energy(), -.243349E+02)
        # FeH3 (HCP10*A3B6*OP)
        matrix = Matrix(conc, unitcell, ecis, 3,
                        order=[0, 0, 0, 0, 0, 0, 1, 1, 1])
        assert np.allclose(matrix.get_energy(), -.848994E+02)
        # FeH5 (HCP99998*A5B4*OP)
        matrix = Matrix(conc, unitcell, ecis, 4,
                        order=[1, 0, 1, 0, 1, 0, 1, 0, 1])
        assert np.allclose(matrix.get_energy(), -.565030E+02)
        # FeH6 (HCP99997*A6B3*OP)
        matrix = Matrix(conc, unitcell, ecis, 5,
                        order=[1, 1, 1, 0, 0, 0, 1, 1, 1])
        assert np.allclose(matrix.get_energy(), -.100641E+03)

        # get_de
        matrix = Matrix(conc, unitcell, ecis, 5)
        # [0, 0, 0, 0] のみの de
        de = matrix.get_delta_energy([[[[True]]]])
        # 全てのサイト
        de_matrix = matrix.get_delta_energy(
            matrix.matrix[:, :, :, :] != 0.5).reshape(5, 5, 5, 9)
        before = matrix.get_energy()
        matrix.matrix[0, 0, 0, 0] = 1 - matrix.matrix[0, 0, 0, 0]
        after = matrix.get_energy()
        assert np.allclose(de, (after - before)*(matrix.matrix.size))
        assert np.allclose(de_matrix[0, 0, 0, 0],
                           (after - before)*(matrix.matrix.size))

        # adjust_conc_fine
        ## 160329
        matrix = Matrix(conc, unitcell, ecis, 4)
        matrix.adjust_conc_fine(conc)
        assert matrix.conc == 0.5
コード例 #6
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    def test_Ecis(self):
        """ Ecis """
        path = os.path.join(self.PATH, "Ecis")
        unitcell = UnitCell.from_file(os.path.join(path, "log.txt"))
        # parse_ecitxt
        ## 160305
        ecis = Ecis.parse_ecitxt(os.path.join(path, "eci.txt"))
        out = {0: 0.680236051, 1: -673.192307, 2: -208.572905, 3: 1752.08986,
               4: 306.073297, 5: 147.11169, 6: 129.361349, 7: 233.347231,
               8: 237.242402, 9: -4.14835143, 10: -44.2051374, 11: -1652.97108,
               12: -286.755208, 13: -668.664112, 14: -714.67382, 16: 1227.364,
               17: -707.7569, 19: -8.39681819, 20: -20.1496428, 22: 26.7883166,
               24: -118.547219, 26: -6.21356756, 27: 1404.19369, 28: 1180.73395,
               29: 95.1228157, 31: 100.481087, 35: -1089.71922, 36: 150.635303,
               38: -845.97957, 44: -312.645058, 45: -134.730871, 47: -244.485361,
               48: -117.505334, 49: 444.617266, 52: 294.931568, 53: -274.314461,
               54: 407.711243}
        assert ecis == out
        # parse_logtxt
        ## 160305
        clus = Ecis.parse_logtxt(os.path.join(path, "log.txt"))
        assert len(clus) == 54
        out = np.array([[0.75, 0.5, 0.25], [0.5, 0.25, -0.25]])
        assert (clus[3] == out).all()

        # get_clusters_from_logtxt
        ## 160306
        clus = Ecis.get_clusters_from_logtxt(os.path.join(path, "log.txt"))
        assert len(clus) == 54
        for i in range(len(clus)):
            for idx in clus[i]:
                equiv = unitcell.symm['equivalent_atoms'][idx]
                assert len(clus[i][idx]) == len(clus[i][equiv])
        # get_diff_clusters
        ## 160306
        out = Ecis.get_diff_clusters(os.path.join(path, "eci.txt"),
                                     os.path.join(path, "log.txt"),
                                     os.path.join(path, "logN6.txt"),
                                     msg=False)
        test = ("16 13 11 0 44 3 17 24 7 29 2 4 19 34 45 36 9 21 1 54 \n"
                "26 5 6 49 15 48 8 10 53 52 27 12 28 47 20 38 31 \n")
        assert out.split() == test.split()
        # form_dirc
        ## 160308
        ecis = Ecis.from_dirc(path)

        # Al-Cu_TO_P
        ## 160330
        """
        BRAV=F の構造だとうまくいかない
        log.txt の構造表記の部分は P, F で変化しないが、
        cluster を記述する後半の部分が変わるので、そこで齟齬が生じる
        """
        path = os.path.join(self.PATH, "Ecis", "Al-Cu_TO_P")
        # path = os.path.join(self.PATH, "Ecis", "Al-Cu_TO_F")

        unitcell = UnitCell.from_file(os.path.join(path, "log.txt"))
        ecis = Ecis.parse_ecitxt(os.path.join(path, "eci.txt"))
        clus = Ecis.parse_logtxt(os.path.join(path, "log.txt"))
        # print(clus)
        clus = Ecis.get_clusters_from_logtxt(os.path.join(path, "log.txt"))