Пример #1
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def test_uig_eval_spline_0d_random():
    cs = get_cosine_spline()

    for i in xrange(15):
        origin = np.random.uniform(-1, 1, 3)
        grid_cell = get_random_cell(0.2, 3)
        shape = np.random.randint(10, 20, 3)
        pbc = np.array([0, 0, 0])
        uig = UniformGrid(origin, grid_cell.rvecs, shape, pbc)

        center = np.random.uniform(0, 2, 3)
        output1 = np.zeros(uig.shape)
        uig.eval_spline(cs, center, output1)

        x, y, z = np.indices(shape)
        x = x.ravel()
        y = y.ravel()
        z = z.ravel()
        rvecs = grid_cell.rvecs
        points = np.outer(x, rvecs[0]) + np.outer(y, rvecs[1]) + np.outer(z, rvecs[2])
        points += origin
        distances = np.sqrt(((points-center)**2).sum(axis=1))
        output2 = cs(distances)
        output2.shape = shape

        assert abs(output1 - output2).max() < 1e-10
Пример #2
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def test_cell():
    for i in xrange(12):
        chk = h5.File('horton.test.test_checkpoint.test_cell_%i' % i, driver='core', backing_store=False)
        cell1 = get_random_cell(1.0, i%4)
        coordinates = np.random.uniform(-1, 1, (5, 3))
        numbers = np.random.randint(1, 11, 5)
        sys1 = System(coordinates, numbers, cell=cell1, chk=chk)
        del sys1
        sys2 = System.from_file(chk)
        assert (sys2.cell.rvecs == cell1.rvecs).all()
        chk.close()
Пример #3
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def setup_ranges_rcut(nvec):
    a = 10**np.random.uniform(-1, 1)
    cell = get_random_cell(a, nvec)

    origin = np.random.uniform(-3 * a, 3 * a, 3)
    center = np.random.uniform(-3 * a, 3 * a, 3)
    rcut = np.random.uniform(0.2 * a, 5 * a)

    ranges_begin, ranges_end = cell.get_ranges_rcut(origin - center, rcut)
    ranges_low = ranges_begin - 2
    ranges_high = ranges_end + 2

    return cell, origin, center, rcut, ranges_begin, ranges_end, ranges_low, ranges_high
Пример #4
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def test_load_dump_consistency():
    sys0 = System.from_file(context.get_fn('test/water_element.xyz'))
    sys0._cell = get_random_cell(5.0, 3)

    with tmpdir('horton.io.test.test_vasp.test_load_dump_consistency') as dn:
        sys0.to_file('%s/POSCAR' % dn)
        sys1 = System.from_file('%s/POSCAR' % dn)

    assert (sys1.numbers == [8, 1, 1]).all()
    assert abs(sys0.coordinates[1] - sys1.coordinates[0]).max() < 1e-10
    assert abs(sys0.coordinates[0] - sys1.coordinates[1]).max() < 1e-10
    assert abs(sys0.coordinates[2] - sys1.coordinates[2]).max() < 1e-10
    assert abs(sys0.cell.rvecs - sys1.cell.rvecs).max() < 1e-10
Пример #5
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def setup_ranges_rcut(nvec):
    a = 10**np.random.uniform(-1, 1)
    cell = get_random_cell(a, nvec)

    origin = np.random.uniform(-3*a, 3*a, 3)
    center = np.random.uniform(-3*a, 3*a, 3)
    rcut = np.random.uniform(0.2*a, 5*a)

    ranges_begin, ranges_end = cell.get_ranges_rcut(origin-center, rcut)
    ranges_low = ranges_begin-2
    ranges_high = ranges_end+2

    return cell, origin, center, rcut, ranges_begin, ranges_end, ranges_low, ranges_high
Пример #6
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def test_load_dump_consistency():
    sys0 = System.from_file(context.get_fn('test/water_element.xyz'))
    sys0._cell = get_random_cell(5.0, 3)

    with tmpdir('horton.io.test.test_vasp.test_load_dump_consistency') as dn:
        sys0.to_file('%s/POSCAR' % dn)
        sys1 = System.from_file('%s/POSCAR' % dn)

    assert (sys1.numbers == [8, 1, 1]).all()
    assert abs(sys0.coordinates[1] - sys1.coordinates[0]).max() < 1e-10
    assert abs(sys0.coordinates[0] - sys1.coordinates[1]).max() < 1e-10
    assert abs(sys0.coordinates[2] - sys1.coordinates[2]).max() < 1e-10
    assert abs(sys0.cell.rvecs - sys1.cell.rvecs).max() < 1e-10
Пример #7
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def setup_select_inside(nvec):
    a = 10**np.random.uniform(-1, 1)
    grid_cell = get_random_cell(a, nvec)

    nrep = 40
    shape = np.array([nrep] * nvec)
    pbc = np.random.randint(0, 2, nvec)
    origin = np.random.uniform(-0.5 * nrep * a, 1.5 * nrep * a, 3)
    center = np.random.uniform(0, nrep * a, 3)
    rcut = np.random.uniform(0.1 * nrep * a)

    ranges_begin, ranges_end = grid_cell.get_ranges_rcut(origin - center, rcut)

    return grid_cell, origin, center, rcut, shape, pbc, ranges_begin, ranges_end
Пример #8
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def test_symmetry_attrs():
    generators = np.random.uniform(-1, 1, (5, 3, 4))
    fracs = np.random.uniform(0, 1, (4, 3))
    numbers = np.array([1, 6, 6, 1])
    cell = get_random_cell(10.0, 3)
    s = Symmetry('boo', generators, fracs, numbers, cell)
    assert (s.labels == ['H0', 'C1', 'C2', 'H3']).all()
    s = Symmetry('boo', generators, fracs, numbers, cell, ['q', 'w', 'e', 'r'])
    assert s.name == 'boo'
    assert (s.generators == generators).all()
    assert s.natom == 4
    assert s.fracs is s.fracs
    assert s.numbers is numbers
    assert s.cell is cell
Пример #9
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def test_load_dump_consistency():
    mol0 = IOData.from_file(context.get_fn('test/water_element.xyz'))
    mol0.cell = get_random_cell(5.0, 3)

    with tmpdir('horton.io.test.test_vasp.test_load_dump_consistency') as dn:
        mol0.to_file('%s/POSCAR' % dn)
        mol1 = IOData.from_file('%s/POSCAR' % dn)

    assert mol0.title == mol1.title
    assert (mol1.numbers == [8, 1, 1]).all()
    assert abs(mol0.coordinates[1] - mol1.coordinates[0]).max() < 1e-10
    assert abs(mol0.coordinates[0] - mol1.coordinates[1]).max() < 1e-10
    assert abs(mol0.coordinates[2] - mol1.coordinates[2]).max() < 1e-10
    assert abs(mol0.cell.rvecs - mol1.cell.rvecs).max() < 1e-10
Пример #10
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def test_symmetry_attrs():
    generators = np.random.uniform(-1, 1, (5, 3, 4))
    fracs = np.random.uniform(0, 1, (4, 3))
    numbers = np.array([1, 6, 6, 1])
    cell = get_random_cell(10.0, 3)
    s = Symmetry('boo', generators, fracs, numbers, cell)
    assert (s.labels == ['H0', 'C1', 'C2', 'H3']).all()
    s = Symmetry('boo', generators, fracs, numbers, cell, ['q', 'w', 'e', 'r'])
    assert s.name == 'boo'
    assert (s.generators == generators).all()
    assert s.natom == 4
    assert s.fracs is s.fracs
    assert s.numbers is numbers
    assert s.cell is cell
Пример #11
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def test_symmetry_attrs():
    generators = np.random.uniform(-1, 1, (5, 3, 4))
    fracs = np.random.uniform(0, 1, (4, 3))
    numbers = np.array([1, 6, 6, 1])
    cell = get_random_cell(10.0, 3)
    s = Symmetry("boo", generators, fracs, numbers, cell)
    assert (s.labels == ["H0", "C1", "C2", "H3"]).all()
    s = Symmetry("boo", generators, fracs, numbers, cell, ["q", "w", "e", "r"])
    assert s.name == "boo"
    assert (s.generators == generators).all()
    assert s.natom == 4
    assert s.fracs is s.fracs
    assert s.numbers is numbers
    assert s.cell is cell
Пример #12
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def test_pair_ewald3d_invariance_rcut():
    np.random.seed(0)
    alpha_scale = 4.5
    gcut_scale = 1.5
    delta = np.random.normal(0, 1, 3)
    delta /= np.linalg.norm(delta)
    cell = get_random_cell(1.0, 3)
    results = []
    for rcut in np.arange(10.0, 20.001, 1.0):
        alpha = alpha_scale / rcut
        gcut = gcut_scale * alpha
        results.append(pair_ewald(delta, cell, rcut, alpha, gcut))
    results = np.array(results)
    assert abs(results - results.mean()).max() < 1e-7
Пример #13
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def test_load_dump_consistency():
    mol0 = IOData.from_file(context.get_fn('test/water_element.xyz'))
    mol0.cell = get_random_cell(5.0, 3)

    with tmpdir('horton.io.test.test_vasp.test_load_dump_consistency') as dn:
        mol0.to_file('%s/POSCAR' % dn)
        mol1 = IOData.from_file('%s/POSCAR' % dn)

    assert mol0.title == mol1.title
    assert (mol1.numbers == [8, 1, 1]).all()
    assert abs(mol0.coordinates[1] - mol1.coordinates[0]).max() < 1e-10
    assert abs(mol0.coordinates[0] - mol1.coordinates[1]).max() < 1e-10
    assert abs(mol0.coordinates[2] - mol1.coordinates[2]).max() < 1e-10
    assert abs(mol0.cell.rvecs - mol1.cell.rvecs).max() < 1e-10
Пример #14
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def test_pair_ewald3d_invariance_rcut():
    np.random.seed(0)
    alpha_scale = 4.5
    gcut_scale = 1.5
    delta = np.random.normal(0, 1, 3)
    delta /= np.linalg.norm(delta)
    cell = get_random_cell(1.0, 3)
    results = []
    for rcut in np.arange(10.0, 20.001, 1.0):
        alpha = alpha_scale/rcut
        gcut = gcut_scale*alpha
        results.append(pair_ewald(delta, cell, rcut, alpha, gcut))
    results = np.array(results)
    assert abs(results - results.mean()).max() < 1e-7
Пример #15
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def setup_select_inside(nvec):
    a = 10**np.random.uniform(-1, 1)
    grid_cell = get_random_cell(a, nvec)

    nrep = 40
    shape = np.array([nrep]*nvec)
    pbc = np.random.randint(0, 2, nvec)
    origin = np.random.uniform(-0.5*nrep*a, 1.5*nrep*a, 3)
    center = np.random.uniform(0, nrep*a, 3)
    rcut = np.random.uniform(0.1*nrep*a)

    ranges_begin, ranges_end = grid_cell.get_ranges_rcut(origin-center, rcut)

    return grid_cell, origin, center, rcut, shape, pbc, ranges_begin, ranges_end
Пример #16
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def test_eval_spline_grid_3d_random():
    npoint = 10
    for i in xrange(10):
        cell = get_random_cell(1.0, 3)
        rvecs = cell.rvecs
        points = np.dot(np.random.normal(-2, 3, (npoint, 3)), rvecs)
        g = IntGrid(points, np.random.normal(0, 1.0, npoint))
        cs = get_cosine_spline()

        output1 = np.zeros(npoint)
        center1 = np.random.uniform(-10, 10, 3)
        g.eval_spline(cs, center1, output1, cell)
        output2 = np.zeros(npoint)
        center2 = center1 + np.dot(np.random.randint(-3, 3, 3), rvecs)
        g.eval_spline(cs, center2, output2, cell)

        assert abs(output1 - output2).max() < 1e-10
Пример #17
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def test_eval_spline_grid_3d_random():
    npoint = 10
    for i in xrange(10):
        cell = get_random_cell(1.0, 3)
        rvecs = cell.rvecs
        points = np.dot(np.random.normal(-2, 3, (npoint,3)), rvecs)
        g = IntGrid(points, np.random.normal(0, 1.0, npoint))
        cs = get_cosine_spline()

        output1 = np.zeros(npoint)
        center1 = np.random.uniform(-10, 10, 3)
        g.eval_spline(cs, center1, output1, cell)
        output2 = np.zeros(npoint)
        center2 = center1 + np.dot(np.random.randint(-3, 3, 3), rvecs)
        g.eval_spline(cs, center2, output2, cell)

        assert abs(output1 - output2).max() < 1e-10
Пример #18
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def test_uig_eval_spline_3d_random():
    cs = get_cosine_spline()

    for i in xrange(30):
        origin = np.random.uniform(-1, 1, 3)
        grid_cell = get_random_cell(0.3, 3)
        shape = np.random.randint(10, 20, 3)
        pbc = np.array([1, 1, 1])
        uig = UniformGrid(origin, grid_cell.rvecs, shape, pbc)

        rvecs = uig.get_cell().rvecs

        output1 = np.zeros(uig.shape)
        center1 = np.random.uniform(-3, 3, 3)
        uig.eval_spline(cs, center1, output1)
        output2 = np.zeros(uig.shape)
        center2 = center1 + np.dot(np.random.randint(-3, 3, 3), rvecs)
        uig.eval_spline(cs, center2, output2)

        assert abs(output1 - output2).max() < 1e-10
Пример #19
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def test_eval_spline_grid_add_random():
    npoint = 10
    cs = get_cosine_spline()

    for i in xrange(10):
        cell = get_random_cell(1.0, np.random.randint(4))
        points = np.random.normal(-2, 3, (npoint,3))
        g = IntGrid(points, np.random.normal(0, 1.0, npoint))

        output1 = np.zeros(npoint)
        center1 = np.random.uniform(-2, 2, 3)
        g.eval_spline(cs, center1, output1, cell)

        output2 = np.zeros(npoint)
        center2 = np.random.uniform(-2, 2, 3)
        g.eval_spline(cs, center2, output2, cell)

        output3 = np.zeros(npoint)
        g.eval_spline(cs, center1, output3, cell)
        g.eval_spline(cs, center2, output3, cell)

        assert abs(output1 + output2 - output3).max() < 1e-10
Пример #20
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def test_uig_eval_spline_1d_random():
    cs = get_cosine_spline()

    for i in xrange(15):
        origin = np.random.uniform(-1, 1, 3)
        grid_cell = get_random_cell(0.2, 3)
        shape = np.random.randint(10, 20, 3)
        pbc = np.array([0, 0, 0])
        pbc[np.random.randint(3)] = 1
        uig = UniformGrid(origin, grid_cell.rvecs, shape, pbc)

        tmp = uig.shape*pbc
        rvecs = grid_cell.rvecs*tmp.reshape(-1,1)

        output1 = np.zeros(uig.shape)
        center1 = np.random.uniform(0, 1, 3)
        uig.eval_spline(cs, center1, output1)
        output2 = np.zeros(uig.shape)
        center2 = center1 + np.dot(np.random.randint(-3, 3, 3), rvecs)
        uig.eval_spline(cs, center2, output2)

        assert abs(output1 - output2).max() < 1e-10
Пример #21
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def test_eval_spline_grid_add_random():
    npoint = 10
    cs = get_cosine_spline()

    for i in xrange(10):
        cell = get_random_cell(1.0, np.random.randint(4))
        points = np.random.normal(-2, 3, (npoint, 3))
        g = IntGrid(points, np.random.normal(0, 1.0, npoint))

        output1 = np.zeros(npoint)
        center1 = np.random.uniform(-2, 2, 3)
        g.eval_spline(cs, center1, output1, cell)

        output2 = np.zeros(npoint)
        center2 = np.random.uniform(-2, 2, 3)
        g.eval_spline(cs, center2, output2, cell)

        output3 = np.zeros(npoint)
        g.eval_spline(cs, center1, output3, cell)
        g.eval_spline(cs, center2, output3, cell)

        assert abs(output1 + output2 - output3).max() < 1e-10
Пример #22
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def test_uig_eval_spline_add_random():
    cs = get_cosine_spline()

    for i in xrange(20):
        origin = np.random.uniform(-1, 1, 3)
        grid_cell = get_random_cell(0.2, 3)
        shape = np.random.randint(10, 20, 3)
        pbc = np.random.randint(0, 2, 3).astype(int)
        uig = UniformGrid(origin, grid_cell.rvecs, shape, pbc)

        output1 = np.zeros(uig.shape)
        center1 = np.random.uniform(0, 1, 3)
        uig.eval_spline(cs, center1, output1)

        output2 = np.zeros(uig.shape)
        center2 = np.random.uniform(0, 1, 3)
        uig.eval_spline(cs, center2, output2)

        output3 = np.zeros(uig.shape)
        uig.eval_spline(cs, center1, output3)
        uig.eval_spline(cs, center2, output3)

        assert abs(output1 + output2 - output3).max() < 1e-10
Пример #23
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def test_from_parameters3():
    for i in xrange(10):
        cell0 = get_random_cell(1.0, 3)
        check_from_parameters(cell0)
Пример #24
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def test_from_parameters3():
    for i in xrange(10):
        cell0 = get_random_cell(1.0, 3)
        check_from_parameters(cell0)