Python read_pwscfの例

コード例 #1

ファイル: __init__.py プロジェクト: shahramyalameha/phonopy

def read_crystal_structure(filename=None,
                           interface_mode=None,
                           chemical_symbols=None,
                           yaml_mode=False):
    if filename is None:
        unitcell_filename = get_default_cell_filename(interface_mode,
                                                      yaml_mode)
    else:
        unitcell_filename = filename

    if not os.path.exists(unitcell_filename):
        if filename is None:
            return None, (unitcell_filename + " (default file name)", )
        else:
            return None, (unitcell_filename, )

    if yaml_mode:
        from phonopy.interface.phonopy_yaml import PhonopyYaml
        phpy_yaml = PhonopyYaml()
        phpy_yaml.read(unitcell_filename)
        unitcell = phpy_yaml.get_unitcell()
        return unitcell, (unitcell_filename, )

    if interface_mode is None or interface_mode == 'vasp':
        from phonopy.interface.vasp import read_vasp
        if chemical_symbols is None:
            unitcell = read_vasp(unitcell_filename)
        else:
            unitcell = read_vasp(unitcell_filename, symbols=chemical_symbols)
        return unitcell, (unitcell_filename, )

    if interface_mode == 'abinit':
        from phonopy.interface.abinit import read_abinit
        unitcell = read_abinit(unitcell_filename)
        return unitcell, (unitcell_filename, )

    if interface_mode == 'pwscf':
        from phonopy.interface.pwscf import read_pwscf
        unitcell, pp_filenames = read_pwscf(unitcell_filename)
        return unitcell, (unitcell_filename, pp_filenames)

    if interface_mode == 'wien2k':
        from phonopy.interface.wien2k import parse_wien2k_struct
        unitcell, npts, r0s, rmts = parse_wien2k_struct(unitcell_filename)
        return unitcell, (unitcell_filename, npts, r0s, rmts)

    if interface_mode == 'elk':
        from phonopy.interface.elk import read_elk
        unitcell, sp_filenames = read_elk(unitcell_filename)
        return unitcell, (unitcell_filename, sp_filenames)

    if interface_mode == 'siesta':
        from phonopy.interface.siesta import read_siesta
        unitcell, atypes = read_siesta(unitcell_filename)
        return unitcell, (unitcell_filename, atypes)

    if interface_mode == 'crystal':
        from phonopy.interface.crystal import read_crystal
        unitcell, conv_numbers = read_crystal(unitcell_filename)
        return unitcell, (unitcell_filename, conv_numbers)

コード例 #2

ファイル: __init__.py プロジェクト: nfh/phonopy

def read_crystal_structure(filename=None, interface_mode="vasp", chemical_symbols=None, yaml_mode=False):
    if filename is None:
        unitcell_filename = get_default_cell_filename(interface_mode, yaml_mode)
    else:
        unitcell_filename = filename

    if not os.path.exists(unitcell_filename):
        if filename is None:
            return None, (unitcell_filename + " (default file name)",)
        else:
            return None, (unitcell_filename,)

    if yaml_mode:
        from phonopy.interface.phonopy_yaml import phonopyYaml

        unitcell = phonopyYaml(unitcell_filename).get_atoms()
        return unitcell, (unitcell_filename,)

    if interface_mode == "vasp":
        from phonopy.interface.vasp import read_vasp

        if chemical_symbols is None:
            unitcell = read_vasp(unitcell_filename)
        else:
            unitcell = read_vasp(unitcell_filename, symbols=chemical_symbols)
        return unitcell, (unitcell_filename,)

    if interface_mode == "abinit":
        from phonopy.interface.abinit import read_abinit

        unitcell = read_abinit(unitcell_filename)
        return unitcell, (unitcell_filename,)

    if interface_mode == "pwscf":
        from phonopy.interface.pwscf import read_pwscf

        unitcell, pp_filenames = read_pwscf(unitcell_filename)
        return unitcell, (unitcell_filename, pp_filenames)

    if interface_mode == "wien2k":
        from phonopy.interface.wien2k import parse_wien2k_struct

        unitcell, npts, r0s, rmts = parse_wien2k_struct(unitcell_filename)
        return unitcell, (unitcell_filename, npts, r0s, rmts)

    if interface_mode == "elk":
        from phonopy.interface.elk import read_elk

        unitcell, sp_filenames = read_elk(unitcell_filename)
        return unitcell, (unitcell_filename, sp_filenames)

    if interface_mode == "siesta":
        from phonopy.interface.siesta import read_siesta

        unitcell, atypes = read_siesta(unitcell_filename)
        return unitcell, (unitcell_filename, atypes)

コード例 #3

def read_crystal_structure(filename=None,
                           interface_mode=None,
                           chemical_symbols=None,
                           yaml_mode=False):
    if filename is None:
        unitcell_filename = get_default_cell_filename(interface_mode, yaml_mode)
    else:
        unitcell_filename = filename

    if not os.path.exists(unitcell_filename):
        if filename is None:
            return None, (unitcell_filename + " (default file name)",)
        else:
            return None, (unitcell_filename,)

    if yaml_mode:
        from phonopy.interface.phonopy_yaml import PhonopyYaml
        phpy_yaml = PhonopyYaml()
        phpy_yaml.read(unitcell_filename)
        unitcell = phpy_yaml.get_unitcell()
        return unitcell, (unitcell_filename,)

    if interface_mode is None or interface_mode == 'vasp':
        from phonopy.interface.vasp import read_vasp
        if chemical_symbols is None:
            unitcell = read_vasp(unitcell_filename)
        else:
            unitcell = read_vasp(unitcell_filename, symbols=chemical_symbols)
        return unitcell, (unitcell_filename,)

    if interface_mode == 'abinit':
        from phonopy.interface.abinit import read_abinit
        unitcell = read_abinit(unitcell_filename)
        return unitcell, (unitcell_filename,)

    if interface_mode == 'pwscf':
        from phonopy.interface.pwscf import read_pwscf
        unitcell, pp_filenames = read_pwscf(unitcell_filename)
        return unitcell, (unitcell_filename, pp_filenames)

    if interface_mode == 'wien2k':
        from phonopy.interface.wien2k import parse_wien2k_struct
        unitcell, npts, r0s, rmts = parse_wien2k_struct(unitcell_filename)
        return unitcell, (unitcell_filename, npts, r0s, rmts)

    if interface_mode == 'elk':
        from phonopy.interface.elk import read_elk
        unitcell, sp_filenames = read_elk(unitcell_filename)
        return unitcell, (unitcell_filename, sp_filenames)

    if interface_mode == 'siesta':
        from phonopy.interface.siesta import read_siesta
        unitcell, atypes = read_siesta(unitcell_filename)
        return unitcell, (unitcell_filename, atypes)

コード例 #4

ファイル: test_pwscf.py プロジェクト: matk86/phonopy

 def test_read_pwscf(self):
     cell, pp_filenames = read_pwscf("NaCl-pwscf.in")
     cell_ref = get_unitcell_from_phonopy_yaml("NaCl-pwscf.yaml")
     self.assertTrue(
         (np.abs(cell.get_cell() - cell_ref.get_cell()) < 1e-5).all())
     diff_pos = cell.get_scaled_positions() - cell_ref.get_scaled_positions()
     diff_pos -= np.rint(diff_pos)
     self.assertTrue((np.abs(diff_pos) < 1e-5).all())
     for s, s_r in zip(cell.get_chemical_symbols(),
                       cell_ref.get_chemical_symbols()): 
         self.assertTrue(s == s_r)

コード例 #5

 def test_read_pwscf(self):
     cell, pp_filenames = read_pwscf(os.path.join(data_dir,"NaCl-pwscf.in"))
     filename = os.path.join(data_dir,"NaCl-abinit-pwscf.yaml")
     cell_ref = get_unitcell_from_phonopy_yaml(filename)
     self.assertTrue(
         (np.abs(cell.get_cell() - cell_ref.get_cell()) < 1e-5).all())
     diff_pos = cell.get_scaled_positions() - cell_ref.get_scaled_positions()
     diff_pos -= np.rint(diff_pos)
     self.assertTrue((np.abs(diff_pos) < 1e-5).all())
     for s, s_r in zip(cell.get_chemical_symbols(),
                       cell_ref.get_chemical_symbols()):
         self.assertTrue(s == s_r)

コード例 #6

ファイル: __init__.py プロジェクト: FermiSea/phonopy

def read_crystal_structure(filename=None,
                           interface_mode='vasp',
                           chemical_symbols=None):
    if filename is None:
        unitcell_filename = get_default_cell_filename(interface_mode)
    else:
        unitcell_filename = filename

    if not os.path.exists(unitcell_filename):
        if filename is None:
            return None, (unitcell_filename + " (default file name)", )
        else:
            return None, (unitcell_filename, )

    if interface_mode == 'vasp':
        from phonopy.interface.vasp import read_vasp
        if chemical_symbols is None:
            unitcell = read_vasp(unitcell_filename)
        else:
            unitcell = read_vasp(unitcell_filename, symbols=chemical_symbols)
        return unitcell, (unitcell_filename, )

    if interface_mode == 'abinit':
        from phonopy.interface.abinit import read_abinit
        unitcell = read_abinit(unitcell_filename)
        return unitcell, (unitcell_filename, )

    if interface_mode == 'pwscf':
        from phonopy.interface.pwscf import read_pwscf
        unitcell, pp_filenames = read_pwscf(unitcell_filename)
        return unitcell, (unitcell_filename, pp_filenames)

    if interface_mode == 'wien2k':
        from phonopy.interface.wien2k import parse_wien2k_struct
        unitcell, npts, r0s, rmts = parse_wien2k_struct(unitcell_filename)
        return unitcell, (unitcell_filename, npts, r0s, rmts)

コード例 #7

ファイル: __init__.py プロジェクト: Maofei/phonopy

def read_crystal_structure(filename=None,
                           interface_mode='vasp',
                           chemical_symbols=None):
    if filename is None:
        unitcell_filename = get_default_cell_filename(interface_mode)
    else:
        unitcell_filename = filename

    if not os.path.exists(unitcell_filename):
        if filename is None:
            return None, (unitcell_filename + " (default file name)",)
        else:
            return None, (unitcell_filename,)
    
    if interface_mode == 'vasp':
        from phonopy.interface.vasp import read_vasp
        if chemical_symbols is None:
            unitcell = read_vasp(unitcell_filename)
        else:
            unitcell = read_vasp(unitcell_filename, symbols=chemical_symbols)
        return unitcell, (unitcell_filename,)
        
    if interface_mode == 'abinit':
        from phonopy.interface.abinit import read_abinit
        unitcell = read_abinit(unitcell_filename)
        return unitcell, (unitcell_filename,)
        
    if interface_mode == 'pwscf':
        from phonopy.interface.pwscf import read_pwscf
        unitcell, pp_filenames = read_pwscf(unitcell_filename)
        return unitcell, (unitcell_filename, pp_filenames)
        
    if interface_mode == 'wien2k':
        from phonopy.interface.wien2k import parse_wien2k_struct
        unitcell, npts, r0s, rmts = parse_wien2k_struct(unitcell_filename)
        return unitcell, (unitcell_filename, npts, r0s, rmts)