Esempio n. 1
0
File: cif.py Progetto: atztogo/cogue
def write_cif_P1(cell, filename=None):
    a, b, c = get_lattice_parameters(cell.lattice)
    alpha, beta, gamma = get_angles(cell.lattice)

    cif = """data_cogue_crystal_converter

_symmetry_space_group_name_H-M     'P 1'
_symmetry_Int_Tables_number        1

_cell_length_a                     %.5f
_cell_length_b                     %.5f
_cell_length_c                     %.5f
_cell_angle_alpha                  %.5f
_cell_angle_beta                   %.5f
_cell_angle_gamma                  %.5f
_cell_volume                       %.5f
_cell_formula_units_Z              1

loop_
_space_group_symop_operation_xyz
x,y,z

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy\n""" % (a, b, c, alpha, beta, gamma, cell.get_volume())

    symbols = []
    for s, p in zip(cell.get_symbols(), cell.get_points().T):
        symbols.append(s)
        cif += ("%-7s%2s %10.5f%10.5f%10.5f   1.00000\n" %
                (s + "%d" % symbols.count(s), s, p[0], p[1], p[2]))

    if filename is None:
        return cif
    else:
        w = open(filename, 'w')
        w.write(cif)
        w.close()
Esempio n. 2
0

if __name__ == "__main__":
    import sys
    import yaml
    from phonopy import Phonopy
    from phonopy.interface.phonopy_yaml import phonopyYaml
    from phonopy.file_IO import parse_FORCE_SETS
    from cogue.crystal.utility import get_angles, get_lattice_parameters
    import matplotlib

    if len(sys.argv) > 1:
        cell = phonopyYaml(sys.argv[1]).get_atoms()
    else:
        cell = phonopyYaml("POSCAR-unitcell.yaml").get_atoms()
    phonon_info = yaml.load(open("phonon.yaml"))
    phonon = Phonopy(cell, phonon_info["supercell_matrix"], is_auto_displacements=False)
    force_sets = parse_FORCE_SETS()
    phonon.set_displacement_dataset(force_sets)
    phonon.produce_force_constants()

    distance = 200
    imaginary = Imaginary(phonon, distance=distance)

    lattice = imaginary.get_lattice()
    print "lattice_lengths: [ %f, %f, %f ]" % tuple(get_lattice_parameters(lattice))
    print "lattice_angles: [ %f, %f, %f ]" % tuple(get_angles(lattice))
    print "mesh_length: %f" % distance
    print "mesh: [ %d, %d, %d ]" % tuple(imaginary.get_mesh())
    print "ratio: %f" % imaginary.get_imaginary_qpoint_ratio()
Esempio n. 3
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    phonons = []
    for dirname in ('gruneisen-01', 'gruneisen-02', 'gruneisen-00'):
        if len(sys.argv) > 1:
            cell = phonopyYaml("%s/" % dirname + sys.argv[1]).get_atoms()
        else:
            cell = phonopyYaml("%s/POSCAR-unitcell.yaml" % dirname).get_atoms()
        phonon_info = yaml.load(open("%s/phonon.yaml" % dirname))
        phonon = Phonopy(cell,
                         phonon_info['supercell_matrix'],
                         is_auto_displacements=False)
        force_sets = parse_FORCE_SETS(filename="%s/FORCE_SETS" % dirname)
        phonon.set_displacement_dataset(force_sets)
        phonon.produce_force_constants()
        phonons.append(phonon)

    phonopy_gruneisen = PhonopyGruneisen(phonons[0], phonons[1], phonons[2])
    distance = 200
    gruneisen = ModeGruneisen(phonopy_gruneisen,
                              distance=distance)
    if gruneisen.run():
        gruneisen.plot(plt)
        lattice = gruneisen.get_lattice()
        print "a, b, c =", get_lattice_parameters(lattice)
        print "alpha, beta, gamma =", get_angles(lattice)
        print "mesh (x=%f) =" % distance, gruneisen.get_mesh()
        gruneisen.save_figure(plt)
        # plt.show()
    else:
        print "Mode Gruneisen parameter calculation failed."
Esempio n. 4
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    import matplotlib

    matplotlib.use('Agg')            
    matplotlib.rcParams.update({'figure.figsize': (4.5, 3),
                                'font.family': 'serif'})
    import matplotlib.pyplot as plt
    
    if len(sys.argv) > 1:
        cell = phonopyYaml(sys.argv[1]).get_atoms()
    else:
        cell = phonopyYaml("POSCAR-unitcell.yaml").get_atoms()
    phonon_info = yaml.load(open("phonon.yaml"))
    phonon = Phonopy(cell,
                     phonon_info['supercell_matrix'],
                     is_auto_displacements=False)
    force_sets = parse_FORCE_SETS()
    phonon.set_displacement_dataset(force_sets)
    phonon.produce_force_constants()
    
    distance = 100
    tprops = ThermalProperty(phonon, distance=distance)
    if tprops.run():
        tprops.plot(plt)
        lattice = tprops.get_lattice()
        print("a, b, c = %f %f %f" % tuple(get_lattice_parameters(lattice)))
        print("alpha, beta, gamma = %f %f %f" % tuple(get_angles(lattice)))
        print("mesh (x=%f) = %s" % (distance, tprops.get_mesh()))
        tprops.save_figure(plt)
    else:
        print "Thermal property calculation failed."