Python Phonopy.get_primitive方法代碼示例

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import get_primitive [as 別名]
def obtain_eigenvectors_from_phonopy(structure, q_vector, NAC=False):

    #   Checking data
    force_atoms_file = structure.get_force_set().item(0)["natom"]
    force_atoms_input = np.product(np.diagonal(structure.get_super_cell_phonon())) * structure.get_number_of_atoms()

    if force_atoms_file != force_atoms_input:
        print("Error: FORCE_SETS file does not match with SUPERCELL MATRIX")
        exit()

    #   Preparing the bulk type object
    bulk = PhonopyAtoms(
        symbols=structure.get_atomic_types(),
        scaled_positions=structure.get_scaled_positions(),
        cell=structure.get_cell().T,
    )

    phonon = Phonopy(
        bulk,
        structure.get_super_cell_phonon(),
        primitive_matrix=structure.get_primitive_matrix(),
        is_auto_displacements=False,
    )

    # Non Analytical Corrections (NAC) from Phonopy [Frequencies only, eigenvectors no affected by this option]
    if NAC:
        print("Phonopy warning: Using Non Analytical Corrections")
        get_is_symmetry = True  # from phonopy:   settings.get_is_symmetry()
        primitive = phonon.get_primitive()
        nac_params = parse_BORN(primitive, get_is_symmetry)
        phonon.set_nac_params(nac_params=nac_params)

    phonon.set_displacement_dataset(copy.deepcopy(structure.get_force_set()))
    phonon.produce_force_constants()

    frequencies, eigenvectors = phonon.get_frequencies_with_eigenvectors(q_vector)

    # Making sure eigenvectors are orthonormal (can be omitted)
    if True:
        eigenvectors = eigenvectors_normalization(eigenvectors)
        print("Testing eigenvectors orthonormality")
        np.set_printoptions(precision=3, suppress=True)
        print(np.dot(eigenvectors.T, np.ma.conjugate(eigenvectors)).real)
        np.set_printoptions(suppress=False)

    # Arranging eigenvectors by atoms and dimensions
    number_of_dimensions = structure.get_number_of_dimensions()
    number_of_primitive_atoms = structure.get_number_of_primitive_atoms()

    arranged_ev = np.array(
        [
            [
                [eigenvectors[j * number_of_dimensions + k, i] for k in range(number_of_dimensions)]
                for j in range(number_of_primitive_atoms)
            ]
            for i in range(number_of_primitive_atoms * number_of_dimensions)
        ]
    )

    return arranged_ev, frequencies

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import get_primitive [as 別名]
 def _get_phonon_NaCl(self):
     cell = read_vasp(os.path.join(data_dir, "..", "POSCAR_NaCl"))
     phonon = Phonopy(cell,
                      np.diag([2, 2, 2]),
                      primitive_matrix=[[0, 0.5, 0.5],
                                        [0.5, 0, 0.5],
                                        [0.5, 0.5, 0]])
     filename = os.path.join(data_dir, "..", "FORCE_SETS_NaCl")
     force_sets = parse_FORCE_SETS(filename=filename)
     phonon.set_displacement_dataset(force_sets)
     phonon.produce_force_constants()
     filename_born = os.path.join(data_dir, "..", "BORN_NaCl")
     nac_params = parse_BORN(phonon.get_primitive(), filename=filename_born)
     phonon.set_nac_params(nac_params)
     return phonon

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import get_primitive [as 別名]
def obtain_phonon_dispersion_spectra(structure, bands_ranges, NAC=False, band_resolution=30):

    print("Calculating phonon dispersion spectra...")
    bulk = PhonopyAtoms(
        symbols=structure.get_atomic_types(),
        scaled_positions=structure.get_scaled_positions(),
        cell=structure.get_cell().T,
    )

    phonon = Phonopy(
        bulk,
        structure.get_super_cell_phonon(),
        primitive_matrix=structure.get_primitive_matrix(),
        is_auto_displacements=False,
    )

    if NAC:
        print("Phonopy warning: Using Non Analitical Corrections")
        print("BORN file is needed to do this")
        get_is_symmetry = True  # sfrom phonopy:   settings.get_is_symmetry()
        primitive = phonon.get_primitive()
        nac_params = parse_BORN(primitive, get_is_symmetry)
        phonon.set_nac_params(nac_params=nac_params)

    phonon.set_displacement_dataset(copy.deepcopy(structure.get_force_set()))
    phonon.produce_force_constants()

    bands = []
    for q_start, q_end in bands_ranges:
        band = []
        for i in range(band_resolution + 1):
            band.append(np.array(q_start) + (np.array(q_end) - np.array(q_start)) / band_resolution * i)
        bands.append(band)
    phonon.set_band_structure(bands)

    return phonon.get_band_structure()

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import get_primitive [as 別名]
phonon = Phonopy(unitcell,
                 [[2, 0, 0],
                  [0, 2, 0],
                  [0, 0, 2]],
                 primitive_matrix=[[0, 0.5, 0.5],
                                   [0.5, 0, 0.5],
                                   [0.5, 0.5, 0]])

symmetry = phonon.get_symmetry()
print "Space group:", symmetry.get_international_table()

force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
primitive = phonon.get_primitive()

# Born effective charges and dielectric constants are read from BORN file.
nac_params = parse_BORN(primitive, filename="BORN")
# Or it can be of course given by hand as follows:
# born = [[[1.08703, 0, 0],
#          [0, 1.08703, 0],
#          [0, 0, 1.08703]],
#         [[-1.08672, 0, 0],
#          [0, -1.08672, 0],
#          [0, 0, -1.08672]]]
# epsilon = [[2.43533967, 0, 0],
#            [0, 2.43533967, 0],
#            [0, 0, 2.43533967]]
# factors = 14.400
# nac_params = {'born': born,

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import get_primitive [as 別名]
print "Space group:", symmetry.get_international_table()

# Read and convert forces and displacements
force_sets = parse_FORCE_SETS(cell.get_number_of_atoms() * 4)
# Sets of forces have to be set before phonon.set_post_process or
# at phonon.set_post_process(..., sets_of_forces=sets_of_forces, ...).
phonon.set_force_sets(force_sets)

# To activate non-analytical term correction.
phonon.set_post_process(primitive_matrix=[[2./3, -1./3, -1./3],
                                          [1./3, 1./3, -2./3],
                                          [1./3, 1./3, 1./3]])

# Parameters for non-analytical term correction can be set
# also after phonon.set_post_process
born = parse_BORN(phonon.get_primitive())
phonon.set_nac_params(born)

# Example to obtain dynamical matrix
dmat = phonon.get_dynamical_matrix_at_q([0,0,0])
print dmat

# Example of band structure calculation
bands = []
q_start = np.array([1./3, 1./3, 0])
q_end = np.array([0, 0, 0])
band = []
for i in range(51):
    band.append(q_start + (q_end - q_start) / 50 * i)
bands.append(band)

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import get_primitive [as 別名]
-1.9721233333333332 0 0 0 -1.9721233333333332 0 0 0 -1.9721233333333332"""

#
# initial settings
#
cell = read_vasp_from_strings(poscar_str)
phonon = Phonopy(cell, np.diag([2, 2, 2]))
force_sets = parse_FORCE_SETS_from_strings(force_sets_str,
                                           cell.get_number_of_atoms() * 8)
phonon.set_force_sets(force_sets)
phonon.set_post_process(primitive_matrix=[[0, 0.5, 0.5],
                                          [0.5, 0, 0.5],
                                          [0.5, 0.5, 0]],
                        is_nac=True)
born_params = parse_BORN_from_strings(born_str,
                                      phonon.get_primitive())
phonon.set_nac_params(born_params)                                      

print phonon.get_symmetry().get_international_table()
primitive = phonon.get_primitive()
reclat = np.linalg.inv(primitive.get_cell())
print reclat

ndiv = 100
band = get_band([0.0, 0.0, 0.0], [0.5, 0.5, 0.0], ndiv)
bands = [band]
phonon.set_band_structure(bands)

#
# Run1
#