Python ase.io方法代碼示例

# 需要導入模塊: import ase [as 別名]
# 或者: from ase import io [as 別名]
def structure_to_atoms(structure):
    """
    Convert a qmpy.Structure to an ase.Atoms

    Example::

        >>> import qmpy.io as io
        >>> structure = io.read('POSCAR')
        >>> atoms = io.ase_mapper.structure_to_atoms(structure)

    """
    if not qmpy.FOUND_ASE:
        print 'ASE must be installed to convert a Structure to an Atoms object'
        return
    atoms = ase.Atoms(
            structure.name,
            cell=structure.cell,
            scaled_positions=structure.coords, 
            magmoms=structure.magmoms)
    return atoms 

# 需要導入模塊: import ase [as 別名]
# 或者: from ase import io [as 別名]
def atoms_to_structure(atoms):
    """
    Convert a qmpy.Structure to an ase.Atoms

    Example::

        >>> import qmpy.io.ase_mapper
        >>> atoms = ase.io.read('POSCAR')
        >>> structure = qmpy.io.ase_mapper.atoms_to_structure(atoms)

    """
    if not qmpy.FOUND_ASE:
        print 'ASE must be installed to convert Atoms object to a Structure'
        return
    struct = Structure()
    struct.cell = atoms.get_cell()
    for a in atoms: 
        atom = Atom()
        atom.coord = a.position
        atom.symbol = a.symbol
        atom.magmom = a.magmom
        atom.direct = False
        struct.add_atom(atom)
    return struct 

# 需要導入模塊: import ase [as 別名]
# 或者: from ase import io [as 別名]
def get_symmetry_dataset(self, symprec=1e-5, angle_tolerance=-1.0):
        """

        Args:
            symprec:
            angle_tolerance:

        Returns:

        https://atztogo.github.io/spglib/python-spglib.html
        """
        lattice = np.array(self.get_cell().T, dtype="double", order="C")
        positions = np.array(
            self.get_scaled_positions(wrap=False), dtype="double", order="C"
        )
        numbers = np.array(self.get_atomic_numbers(), dtype="intc")
        return spglib.get_symmetry_dataset(
            cell=(lattice, positions, numbers),
            symprec=symprec,
            angle_tolerance=angle_tolerance,
        ) 

# 需要導入模塊: import ase [as 別名]
# 或者: from ase import io [as 別名]
def refine_cell(self, symprec=1e-5, angle_tolerance=-1.0):
        """

        Args:
            symprec:
            angle_tolerance:

        Returns:

        https://atztogo.github.io/spglib/python-spglib.html
        """
        lattice = np.array(self.get_cell().T, dtype="double", order="C")
        positions = np.array(
            self.get_scaled_positions(wrap=False), dtype="double", order="C"
        )
        numbers = np.array(self.get_atomic_numbers(), dtype="intc")
        cell, coords, el = spglib.refine_cell(
            cell=(lattice, positions, numbers),
            symprec=symprec,
            angle_tolerance=angle_tolerance,
        )

        return Atoms(
            symbols=list(self.get_chemical_symbols()), positions=coords, cell=cell
        ) 

# 需要導入模塊: import ase [as 別名]
# 或者: from ase import io [as 別名]
def write(self, filename, format=None, **kwargs):
        """
        Write atoms object to a file.

        see ase.io.write for formats.
        kwargs are passed to ase.io.write.

        Args:
            filename:
            format:
            **kwargs:

        Returns:

        """
        from ase.io import write

        atoms = self.copy()
        atoms.arrays["positions"] = atoms.positions
        write(filename, atoms, format, **kwargs) 

# 需要導入模塊: import ase [as 別名]
# 或者: from ase import io [as 別名]
def pyiron_to_pymatgen(pyiron_obj):
    """
    Convert pyiron atoms object to pymatgen atoms object

    Args:
        pyiron_obj: pyiron atoms object

    Returns:
        pymatgen atoms object
    """
    try:
        from pymatgen.io.ase import AseAtomsAdaptor
    except ImportError:
        raise ValueError("PyMatGen package not yet installed")
    ase_atoms = pyiron_to_ase(pyiron_obj)
    _check_if_simple_atoms(atoms=ase_atoms)
    return AseAtomsAdaptor().get_structure(atoms=ase_atoms, cls=None) 

# 需要導入模塊: import ase [as 別名]
# 或者: from ase import io [as 別名]
def read(source_file, *args, **kwargs):
    """
    Read an input file of various formats.

    Arguments:
        source_file:
            The first argument is a structure file of some format.

    The remaining args and kwargs are passed to the methods called to read the
    structure.

    If the structure name contains "cif" or "POSCAR" it will be read as one of
    these formats. Failing that, the file is passed to the ASE read method, and
    the returned Atoms object is then converted to a Structure.

    Examples::

        >>> io.read(INSTALL_PATH+'/io/files/POSCAR_FCC')
        >>> io.read(INSTALL_PATH+'/io/files/fe3o4.cif')

    """
    try:
        if 'cif' in source_file:
            return cif.read(source_file, *args, **kwargs)
        elif ( 'POSCAR' in source_file or
                'CONTCAR' in source_file ):
            return poscar.read(source_file, *args, **kwargs)
        else:
            return ase.io.read(source_file, *args, **kwargs)
    except:
        try:
            return poscar.read(source_file, *args, **kwargs)
        except Exception:
            pass
        try:
            return cif.read(source_file, *args, **kwargs)
        except Exception:
            pass
    raise FormatNotSupportedError('The file %s is in an unrecognized format\
            and cannot be read' % source_file) 

# 需要導入模塊: import ase [as 別名]
# 或者: from ase import io [as 別名]
def read(filename, **kwargs):
    """
    Uses the ase.io.read method to read in a file, and convert it to a
    qmpy.Structure object. Passes any optional keyword arguments to the
    ase.io.read call.

    """
    if not qmpy.FOUND_ASE:
        print 'ASE must be installed to convert Atoms object to a Structure'
        return

    atoms = ase.io.read(filename, **kwargs)
    return atoms_to_structure(atoms) 

# 需要導入模塊: import ase [as 別名]
# 或者: from ase import io [as 別名]
def get_spacegroup(self, symprec=1e-5, angle_tolerance=-1.0):
        """

        Args:
            symprec:
            angle_tolerance:

        Returns:

        https://atztogo.github.io/spglib/python-spglib.html
        """
        lattice = np.array(self.get_cell(), dtype="double", order="C")
        positions = np.array(
            self.get_scaled_positions(wrap=False), dtype="double", order="C"
        )
        numbers = np.array(self.get_atomic_numbers(), dtype="intc")
        space_group = spglib.get_spacegroup(
            cell=(lattice, positions, numbers),
            symprec=symprec,
            angle_tolerance=angle_tolerance,
        ).split()
        if len(space_group) == 1:
            return {"Number": ast.literal_eval(space_group[0])}
        else:
            return {
                "InternationalTableSymbol": space_group[0],
                "Number": ast.literal_eval(space_group[1]),
            } 

# 需要導入模塊: import ase [as 別名]
# 或者: from ase import io [as 別名]
def setUp(self):
        ani1x = torchani.models.ANI1x()
        self.aev_computer = ani1x.aev_computer
        filename = os.path.join(path, '../tools/generate-unit-test-expect/others/Benzene.cif')
        benzene = ase.io.read(filename)
        self.cell = torch.tensor(benzene.get_cell(complete=True)).float()
        self.pbc = torch.tensor(benzene.get_pbc(), dtype=torch.bool)
        species_to_tensor = torchani.utils.ChemicalSymbolsToInts(['H', 'C', 'N', 'O'])
        self.species = species_to_tensor(benzene.get_chemical_symbols()).unsqueeze(0)
        self.coordinates = torch.tensor(benzene.get_positions()).unsqueeze(0).float()
        _, self.aev = self.aev_computer((self.species, self.coordinates), cell=self.cell, pbc=self.pbc)
        self.natoms = self.aev.shape[1] 

# 需要導入模塊: import ase [as 別名]
# 或者: from ase import io [as 別名]
def __get_final_atoms_object_with_vasp_forces(launch_id):
    '''
    This function will return an ase.Atoms object from a particular
    FireWorks launch ID. It will also make sure that the ase.Atoms object
    will have VASP-calculated forces attached to it.

    Arg:
        launch_id   An integer representing the FireWorks launch ID of the
                    atoms object you want to get
    Returns:
        atoms   ase.Atoms object with the VASP-calculated forces
    '''
    # We will be opening a temporary directory where we will unzip the
    # FireWorks launch directory
    fw_launch_file = (read_rc('fireworks_info.backup_directory') + '/%d.tar.gz' % launch_id)
    temp_loc = __dump_file_to_tmp(fw_launch_file)

    # Load the atoms object and then load the correct (DFT) forces from the
    # OUTCAR/etc info
    try:
        atoms = ase.io.read('%s/slab_relaxed.traj' % temp_loc)
        vasp2 = Vasp2(atoms, restart=True, directory=temp_loc)
        vasp2.read_results()

    # Clean up behind us
    finally:
        subprocess.call('rm -r %s' % temp_loc, shell=True)

    return atoms 

# 需要導入模塊: import ase [as 別名]
# 或者: from ase import io [as 別名]
def write(structure, format='poscar', convention=None, filename=None,
        **kwargs):
    """
    Write the `~qmpy.Structure` object to a file or string.

    Arguments:
        structure: `~qmpy.Structure` object.

    Keyword Arguments:
        format:
            If the format is "poscar" or "cif", call poscar.write or cif.write
            respectively. Otherwise, converts the Structure to a
            :mod:`~ase.Atoms` object and calls the :func:`ase.io.write` method
            with all arguments and keywords passed to that function.

        convention:
            Takes three values, "primitive", "conventional" or None. If
            "primitive" converts the structure to its primitive cell. If
            "conventional" converts the structure to its conventional cell. If
            None, writes the structure as is.

        filename:
            Filename to write to. If None, returns a string.

    Returns:
        None or a string.

    """
    if convention == 'primitive':
        structure.make_primitive()
    elif convention == 'conventional':
        structure.make_conventional()

    def write_or_return(string, filename=None):
        if filename is None:
            return string
        else:
            f = open(filename, 'w')
            f.write(string)
            f.close()

    if format == 'poscar':
        return write_or_return(poscar.write(structure, **kwargs), filename)
    elif format == 'cif':
        return write_or_return(cif.write(structure, **kwargs), filename)
    else:
        return write_or_return(ase_mapper.write(structure, **kwargs), filename)