예제 #1
0
파일: spglib.py 프로젝트: yw-fang/phonopy 
def refine_cell(cell, symprec=1e-5, angle_tolerance=-1.0):
    """Return refined cell.

    The standardized unit cell is returned by a tuple of
    (lattice, positions, numbers).
    If it fails, None is returned.
    """
    _set_no_error()

    lattice, _positions, _numbers, _ = _expand_cell(cell)
    if lattice is None:
        return None

    # Atomic positions have to be specified by scaled positions for spglib.
    num_atom = len(_positions)
    positions = np.zeros((num_atom * 4, 3), dtype='double', order='C')
    positions[:num_atom] = _positions
    numbers = np.zeros(num_atom * 4, dtype='intc')
    numbers[:num_atom] = _numbers
    num_atom_std = spg.refine_cell(lattice, positions, numbers, num_atom,
                                   symprec, angle_tolerance)
    _set_error_message()

    if num_atom_std > 0:
        return (np.array(lattice.T, dtype='double', order='C'),
                np.array(positions[:num_atom_std], dtype='double', order='C'),
                np.array(numbers[:num_atom_std], dtype='intc'))
    else:
        return None
예제 #2
0
파일: spglib.py 프로젝트: gcgs1/phonopy 
def refine_cell(cell, symprec=1e-5, angle_tolerance=-1.0):
    """Return refined cell.

    The standardized unit cell is returned by a tuple of
    (lattice, positions, numbers).
    If it fails, None is returned.
    """
    _set_no_error()

    lattice, _positions, _numbers, _ = _expand_cell(cell)
    if lattice is None:
        return None

    # Atomic positions have to be specified by scaled positions for spglib.
    num_atom = len(_positions)
    positions = np.zeros((num_atom * 4, 3), dtype='double', order='C')
    positions[:num_atom] = _positions
    numbers = np.zeros(num_atom * 4, dtype='intc')
    numbers[:num_atom] = _numbers
    num_atom_std = spg.refine_cell(lattice,
                                   positions,
                                   numbers,
                                   num_atom,
                                   symprec,
                                   angle_tolerance)
    _set_error_message()

    if num_atom_std > 0:
        return (np.array(lattice.T, dtype='double', order='C'),
                np.array(positions[:num_atom_std], dtype='double', order='C'),
                np.array(numbers[:num_atom_std], dtype='intc'))
    else:
        return None
예제 #3
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def refine_cell(bulk, symprec=1e-5, angle_tolerance=-1.0):
    """
    Return refined cell
    """
    # Atomic positions have to be specified by scaled positions for spglib.
    num_atom = bulk.get_number_of_atoms()
    lattice = bulk.get_cell().T.copy()
    pos = np.zeros((num_atom * 4, 3), dtype='double')
    pos[:num_atom] = bulk.get_scaled_positions()

    numbers = np.zeros(num_atom * 4, dtype='intc')
    numbers[:num_atom] = np.intc(bulk.get_atomic_numbers())
    num_atom_bravais = spg.refine_cell(lattice, pos, numbers, num_atom,
                                       symprec, angle_tolerance)

    return (lattice.T.copy(), pos[:num_atom_bravais].copy(),
            numbers[:num_atom_bravais].copy())
예제 #4
0
파일: spglib.py 프로젝트: jasonlarkin/ntpl 
def refine_cell(bulk, symprec=1e-5):
    """
    Return refined cell
    """
    # Atomic positions have to be specified by scaled positions for spglib.
    num_atom = bulk.get_number_of_atoms()
    lattice = bulk.get_cell().T.copy()
    pos = np.zeros( ( num_atom * 4, 3 ), dtype=float )
    pos[:num_atom] = bulk.get_scaled_positions()

    numbers = np.zeros( num_atom * 4, dtype=int )
    numbers[:num_atom] = bulk.get_atomic_numbers()
    num_atom_bravais = spg.refine_cell( lattice,
                                        pos,
                                        numbers,
                                        num_atom,
                                        symprec )

    return lattice.T.copy(), pos[:num_atom_bravais], numbers[:num_atom_bravais]
예제 #5
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def refine_cell(bulk, symprec=1e-5, angle_tolerance=-1.0):
    """
    Return refined cell
    """
    # Atomic positions have to be specified by scaled positions for spglib.
    num_atom = bulk.get_number_of_atoms()
    lattice = np.array(bulk.get_cell().T, dtype='double', order='C')
    pos = np.zeros((num_atom * 4, 3), dtype='double')
    pos[:num_atom] = bulk.get_scaled_positions()

    numbers = np.zeros(num_atom * 4, dtype='intc')
    numbers[:num_atom] = np.array(bulk.get_atomic_numbers(), dtype='intc')
    num_atom_std = spg.refine_cell(lattice, pos, numbers, num_atom, symprec,
                                   angle_tolerance)

    return (np.array(lattice.T, dtype='double', order='C'),
            np.array(pos[:num_atom_std], dtype='double',
                     order='C'), np.array(numbers[:num_atom_std],
                                          dtype='intc'))
예제 #6
0
파일: spglib.py 프로젝트: matk86/phonopy 
def refine_cell(cell, symprec=1e-5, angle_tolerance=-1.0):
    """
    Return refined cell
    """

    lattice, _positions, _numbers, _ = _expand_cell(cell)

    # Atomic positions have to be specified by scaled positions for spglib.
    num_atom = len(_positions)
    positions = np.zeros((num_atom * 4, 3), dtype='double', order='C')
    positions[:num_atom] = _positions
    numbers = np.zeros(num_atom * 4, dtype='intc')
    numbers[:num_atom] = _numbers
    num_atom_std = spg.refine_cell(lattice, positions, numbers, num_atom,
                                   symprec, angle_tolerance)

    return (np.array(lattice.T, dtype='double', order='C'),
            np.array(positions[:num_atom_std], dtype='double',
                     order='C'), np.array(numbers[:num_atom_std],
                                          dtype='intc'))
예제 #7
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def refine_cell(bulk, symprec=1e-5, angle_tolerance=-1.0):
    """
    Return refined cell
    """
    # Atomic positions have to be specified by scaled positions for spglib.
    num_atom = bulk.get_number_of_atoms()
    lattice = np.array(bulk.get_cell().T, dtype='double', order='C')
    pos = np.zeros((num_atom * 4, 3), dtype='double')
    pos[:num_atom] = bulk.get_scaled_positions()

    numbers = np.zeros(num_atom * 4, dtype='intc')
    numbers[:num_atom] = np.array(bulk.get_atomic_numbers(), dtype='intc')
    num_atom_std = spg.refine_cell(lattice,
                                   pos,
                                   numbers,
                                   num_atom,
                                   symprec,
                                   angle_tolerance)

    return (np.array(lattice.T, dtype='double', order='C'),
            np.array(pos[:num_atom_std], dtype='double', order='C'),
            np.array(numbers[:num_atom_std], dtype='intc'))
예제 #8
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def refine_cell(bulk, symprec=1e-5, angle_tolerance=-1.0):
    """
    Return refined cell
    """
    # Atomic positions have to be specified by scaled positions for spglib.
    num_atom = bulk.get_number_of_atoms()
    lattice = bulk.get_cell().T.copy()
    pos = np.zeros((num_atom * 4, 3), dtype='double')
    pos[:num_atom] = bulk.get_scaled_positions()

    numbers = np.zeros(num_atom * 4, dtype='intc')
    numbers[:num_atom] = np.intc(bulk.get_atomic_numbers())
    num_atom_bravais = spg.refine_cell(lattice,
                                       pos,
                                       numbers,
                                       num_atom,
                                       symprec,
                                       angle_tolerance)

    return (lattice.T.copy(),
            pos[:num_atom_bravais].copy(),
            numbers[:num_atom_bravais].copy())
예제 #9
0
파일: spglib.py 프로젝트: chueter/phonopy 
def refine_cell(cell, symprec=1e-5, angle_tolerance=-1.0):
    """
    Return refined cell
    """

    lattice, _positions, _numbers, _ = _expand_cell(cell)

    # Atomic positions have to be specified by scaled positions for spglib.
    num_atom = len(_positions)
    positions = np.zeros((num_atom * 4, 3), dtype='double', order='C')
    positions[:num_atom] = _positions
    numbers = np.zeros(num_atom * 4, dtype='intc')
    numbers[:num_atom] = _numbers
    num_atom_std = spg.refine_cell(lattice,
                                   positions,
                                   numbers,
                                   num_atom,
                                   symprec,
                                   angle_tolerance)

    return (np.array(lattice.T, dtype='double', order='C'),
            np.array(positions[:num_atom_std], dtype='double', order='C'),
            np.array(numbers[:num_atom_std], dtype='intc'))