Exemple #1
0
def read(filename, index=-1, format=None):
    """Read Atoms object(s) from file.

    filename: str
        Name of the file to read from.
    index: int or slice
        If the file contains several configurations, the last configuration
        will be returned by default.  Use index=n to get configuration
        number n (counting from zero).
    format: str
        Used to specify the file-format.  If not given, the
        file-format will be guessed by the *filetype* function.

    Known formats:

    =========================  ===========
    format                     short name
    =========================  ===========
    GPAW restart-file          gpw
    Dacapo netCDF output file  dacapo
    Old ASE netCDF trajectory  nc
    Virtual Nano Lab file      vnl
    ASE pickle trajectory      traj
    ASE bundle trajectory      bundle
    GPAW text output           gpaw-text
    CUBE file                  cube
    XCrySDen Structure File    xsf
    Dacapo text output         dacapo-text
    XYZ-file                   xyz
    VASP POSCAR/CONTCAR file   vasp
    VASP OUTCAR file           vasp_out
    SIESTA STRUCT file         struct_out
    ABINIT input file          abinit
    V_Sim ascii file           v_sim
    Protein Data Bank          pdb
    CIF-file                   cif
    FHI-aims geometry file     aims
    FHI-aims output file       aims_out
    VTK XML Image Data         vti
    VTK XML Structured Grid    vts
    VTK XML Unstructured Grid  vtu
    TURBOMOLE coord file       tmol
    TURBOMOLE gradient file    tmol-gradient
    exciting input             exi
    AtomEye configuration      cfg
    WIEN2k structure file      struct
    DftbPlus input file        dftb
    CASTEP geom file           cell
    CASTEP output file         castep
    CASTEP trajectory file     geom
    ETSF format                etsf.nc
    DFTBPlus GEN format        gen
    CMR db/cmr-file            db
    CMR db/cmr-file            cmr
    LAMMPS dump file           lammps
    =========================  ===========

    """
    if isinstance(filename, str):
        p = filename.rfind('@')
        if p != -1:
            try:
                index = string2index(filename[p + 1:])
            except ValueError:
                pass
            else:
                filename = filename[:p]

    if isinstance(index, str):
        index = string2index(index)

    if format is None:
        format = filetype(filename)

    if format.startswith('gpw'):
        import gpaw
        r = gpaw.io.open(filename, 'r')
        positions = r.get('CartesianPositions') * Bohr
        numbers = r.get('AtomicNumbers')
        cell = r.get('UnitCell') * Bohr
        pbc = r.get('BoundaryConditions')
        tags = r.get('Tags')
        magmoms = r.get('MagneticMoments')
        energy = r.get('PotentialEnergy') * Hartree

        if r.has_array('CartesianForces'):
            forces = r.get('CartesianForces') * Hartree / Bohr
        else:
            forces = None

        atoms = Atoms(positions=positions,
                      numbers=numbers,
                      cell=cell,
                      pbc=pbc)
        if tags.any():
            atoms.set_tags(tags)

        if magmoms.any():
            atoms.set_initial_magnetic_moments(magmoms)
        else:
            magmoms = None

        atoms.calc = SinglePointCalculator(energy, forces, None, magmoms,
                                           atoms)

        return atoms

    if format == 'castep':
        from ase.io.castep import read_castep
        return read_castep(filename, index)

    if format == 'castep_cell':
        import ase.io.castep
        return ase.io.castep.read_cell(filename, index)

    if format == 'castep_geom':
        import ase.io.castep
        return ase.io.castep.read_geom(filename, index)

    if format == 'exi':
        from ase.io.exciting import read_exciting
        return read_exciting(filename, index)

    if format == 'xyz':
        from ase.io.xyz import read_xyz
        return read_xyz(filename, index)

    if format == 'traj':
        from ase.io.trajectory import read_trajectory
        return read_trajectory(filename, index)

    if format == 'bundle':
        from ase.io.bundletrajectory import read_bundletrajectory
        return read_bundletrajectory(filename, index)

    if format == 'cube':
        from ase.io.cube import read_cube
        return read_cube(filename, index)

    if format == 'nc':
        from ase.io.netcdf import read_netcdf
        return read_netcdf(filename, index)

    if format == 'gpaw-text':
        from ase.io.gpawtext import read_gpaw_text
        return read_gpaw_text(filename, index)

    if format == 'dacapo-text':
        from ase.io.dacapo import read_dacapo_text
        return read_dacapo_text(filename)

    if format == 'dacapo':
        from ase.io.dacapo import read_dacapo
        return read_dacapo(filename)

    if format == 'xsf':
        from ase.io.xsf import read_xsf
        return read_xsf(filename, index)

    if format == 'vasp':
        from ase.io.vasp import read_vasp
        return read_vasp(filename)

    if format == 'vasp_out':
        from ase.io.vasp import read_vasp_out
        return read_vasp_out(filename, index)

    if format == 'abinit':
        from ase.io.abinit import read_abinit
        return read_abinit(filename)

    if format == 'v_sim':
        from ase.io.v_sim import read_v_sim
        return read_v_sim(filename)

    if format == 'mol':
        from ase.io.mol import read_mol
        return read_mol(filename)

    if format == 'pdb':
        from ase.io.pdb import read_pdb
        return read_pdb(filename, index)

    if format == 'cif':
        from ase.io.cif import read_cif
        return read_cif(filename, index)

    if format == 'struct':
        from ase.io.wien2k import read_struct
        return read_struct(filename)

    if format == 'struct_out':
        from ase.io.siesta import read_struct
        return read_struct(filename)

    if format == 'vti':
        from ase.io.vtkxml import read_vti
        return read_vti(filename)

    if format == 'vts':
        from ase.io.vtkxml import read_vts
        return read_vts(filename)

    if format == 'vtu':
        from ase.io.vtkxml import read_vtu
        return read_vtu(filename)

    if format == 'aims':
        from ase.io.aims import read_aims
        return read_aims(filename)

    if format == 'aims_out':
        from ase.io.aims import read_aims_output
        return read_aims_output(filename, index)

    if format == 'iwm':
        from ase.io.iwm import read_iwm
        return read_iwm(filename)

    if format == 'Cmdft':
        from ase.io.cmdft import read_I_info
        return read_I_info(filename)

    if format == 'tmol':
        from ase.io.turbomole import read_turbomole
        return read_turbomole(filename)

    if format == 'tmol-gradient':
        from ase.io.turbomole import read_turbomole_gradient
        return read_turbomole_gradient(filename)

    if format == 'cfg':
        from ase.io.cfg import read_cfg
        return read_cfg(filename)

    if format == 'dftb':
        from ase.io.dftb import read_dftb
        return read_dftb(filename)

    if format == 'sdf':
        from ase.io.sdf import read_sdf
        return read_sdf(filename)

    if format == 'etsf':
        from ase.io.etsf import ETSFReader
        return ETSFReader(filename).read_atoms()

    if format == 'gen':
        from ase.io.gen import read_gen
        return read_gen(filename)

    if format == 'db':
        from ase.io.cmr_io import read_db
        return read_db(filename, index)

    if format == 'lammps':
        from ase.io.lammps import read_lammps_dump
        return read_lammps_dump(filename, index)

    raise RuntimeError('File format descriptor '+format+' not recognized!')
Exemple #2
0
def read(filename, index=None, format=None):
    """Read Atoms object(s) from file.

    filename: str
        Name of the file to read from.
    index: int or slice
        If the file contains several configurations, the last configuration
        will be returned by default.  Use index=n to get configuration
        number n (counting from zero).
    format: str
        Used to specify the file-format.  If not given, the
        file-format will be guessed by the *filetype* function.

    Known formats:

    =========================  =============
    format                     short name
    =========================  =============
    GPAW restart-file          gpw
    Dacapo netCDF output file  dacapo
    Old ASE netCDF trajectory  nc
    Virtual Nano Lab file      vnl
    ASE pickle trajectory      traj
    ASE bundle trajectory      bundle
    GPAW text output           gpaw-text
    CUBE file                  cube
    XCrySDen Structure File    xsf
    Dacapo text output         dacapo-text
    XYZ-file                   xyz
    VASP POSCAR/CONTCAR file   vasp
    VASP OUTCAR file           vasp_out
    VASP XDATCAR file          vasp_xdatcar
    SIESTA STRUCT file         struct_out
    ABINIT input file          abinit
    V_Sim ascii file           v_sim
    Protein Data Bank          pdb
    CIF-file                   cif
    FHI-aims geometry file     aims
    FHI-aims output file       aims_out
    VTK XML Image Data         vti
    VTK XML Structured Grid    vts
    VTK XML Unstructured Grid  vtu
    TURBOMOLE coord file       tmol
    TURBOMOLE gradient file    tmol-gradient
    exciting input             exi
    AtomEye configuration      cfg
    WIEN2k structure file      struct
    DftbPlus input file        dftb
    CASTEP geom file           cell
    CASTEP output file         castep
    CASTEP trajectory file     geom
    ETSF format                etsf.nc
    DFTBPlus GEN format        gen
    CMR db/cmr-file            db
    CMR db/cmr-file            cmr
    LAMMPS dump file           lammps
    EON reactant.con file      eon
    Gromacs coordinates        gro
    Gaussian com (input) file  gaussian
    Gaussian output file       gaussian_out
    Quantum espresso in file   esp_in
    Quantum espresso out file  esp_out
    Extended XYZ file          extxyz
    NWChem input file          nw
    Materials Studio file      xsd
    =========================  =============

    Many formats allow on open file-like object to be passed instead
    of ``filename``. In this case the format cannot be auto-decected,
    so the ``format`` argument should be explicitly given.
    
    """
    if isinstance(filename, str) and (
        '[email protected]' in filename or
        '[email protected]' in filename or
        filename.startswith('pg://') and '@' in filename):
        filename, index = filename.rsplit('@', 1)
        if index.isdigit():
            index = int(index)
    else:
        if isinstance(filename, str):
            p = filename.rfind('@')
            if p != -1:
                try:
                    index = string2index(filename[p + 1:])
                except ValueError:
                    pass
                else:
                    filename = filename[:p]

        if isinstance(index, str):
            index = string2index(index)

    if format is None:
        format = filetype(filename)

    if format.startswith('gpw'):
        import gpaw
        r = gpaw.io.open(filename, 'r')
        positions = r.get('CartesianPositions') * Bohr
        numbers = r.get('AtomicNumbers')
        cell = r.get('UnitCell') * Bohr
        pbc = r.get('BoundaryConditions')
        tags = r.get('Tags')
        magmoms = r.get('MagneticMoments')
        energy = r.get('PotentialEnergy') * Hartree

        if r.has_array('CartesianForces'):
            forces = r.get('CartesianForces') * Hartree / Bohr
        else:
            forces = None

        atoms = Atoms(positions=positions,
                      numbers=numbers,
                      cell=cell,
                      pbc=pbc)
        if tags.any():
            atoms.set_tags(tags)

        if magmoms.any():
            atoms.set_initial_magnetic_moments(magmoms)
        else:
            magmoms = None

        atoms.calc = SinglePointDFTCalculator(atoms, energy=energy,
                                              forces=forces, magmoms=magmoms)
        kpts = []
        if r.has_array('IBZKPoints'):
            for w, kpt, eps_n, f_n in zip(r.get('IBZKPointWeights'),
                                          r.get('IBZKPoints'),
                                          r.get('Eigenvalues'),
                                          r.get('OccupationNumbers')):
                kpts.append(SinglePointKPoint(w, kpt[0], kpt[1],
                                              eps_n[0], f_n[0]))
        atoms.calc.kpts = kpts

        return atoms

    if format in ['json', 'db', 'postgresql']:
        if index == slice(None, None):
            index = None
        from ase.db.core import connect
        images = [row.toatoms()
                  for row in connect(filename, format).select(index)]
        if len(images) == 1:
            return images[0]
        else:
            return images

    if index is None:
        index = -1
        
    if format == 'castep':
        from ase.io.castep import read_castep
        return read_castep(filename, index)

    if format == 'castep_cell':
        import ase.io.castep
        return ase.io.castep.read_cell(filename, index)

    if format == 'castep_geom':
        import ase.io.castep
        return ase.io.castep.read_geom(filename, index)

    if format == 'exi':
        from ase.io.exciting import read_exciting
        return read_exciting(filename, index)

    if format in ['xyz', 'extxyz']:
        from ase.io.extxyz import read_xyz
        return read_xyz(filename, index)

    if format == 'traj':
        from ase.io.trajectory import read_trajectory
        return read_trajectory(filename, index)

    if format == 'trj':
        from ase.io.pickletrajectory import read_trajectory
        return read_trajectory(filename, index)

    if format == 'bundle':
        from ase.io.bundletrajectory import read_bundletrajectory
        return read_bundletrajectory(filename, index)

    if format == 'cube':
        from ase.io.cube import read_cube
        return read_cube(filename, index)

    if format == 'nc':
        from ase.io.netcdf import read_netcdf
        return read_netcdf(filename, index)

    if format == 'gpaw-text':
        from ase.io.gpawtext import read_gpaw_text
        return read_gpaw_text(filename, index)

    if format == 'dacapo-text':
        from ase.io.dacapo import read_dacapo_text
        return read_dacapo_text(filename)

    if format == 'dacapo':
        from ase.io.dacapo import read_dacapo
        return read_dacapo(filename)

    if format == 'xsf':
        from ase.io.xsf import read_xsf
        return read_xsf(filename, index)

    if format == 'vasp':
        from ase.io.vasp import read_vasp
        return read_vasp(filename)

    if format == 'vasp_out':
        from ase.io.vasp import read_vasp_out
        return read_vasp_out(filename, index)

    if format == 'vasp_xdatcar':
        from ase.io.vasp import read_vasp_xdatcar
        return read_vasp_xdatcar(filename, index)

    if format == 'abinit':
        from ase.io.abinit import read_abinit
        return read_abinit(filename)

    if format == 'v_sim':
        from ase.io.v_sim import read_v_sim
        return read_v_sim(filename)

    if format == 'mol':
        from ase.io.mol import read_mol
        return read_mol(filename)

    if format == 'pdb':
        from ase.io.pdb import read_pdb
        return read_pdb(filename, index)

    if format == 'cif':
        from ase.io.cif import read_cif
        return read_cif(filename, index)

    if format == 'struct':
        from ase.io.wien2k import read_struct
        return read_struct(filename)

    if format == 'struct_out':
        from ase.io.siesta import read_struct
        return read_struct(filename)

    if format == 'vti':
        from ase.io.vtkxml import read_vti
        return read_vti(filename)

    if format == 'vts':
        from ase.io.vtkxml import read_vts
        return read_vts(filename)

    if format == 'vtu':
        from ase.io.vtkxml import read_vtu
        return read_vtu(filename)

    if format == 'aims':
        from ase.io.aims import read_aims
        return read_aims(filename)

    if format == 'aims_out':
        from ase.io.aims import read_aims_output
        return read_aims_output(filename, index)

    if format == 'iwm':
        from ase.io.iwm import read_iwm
        return read_iwm(filename)

    if format == 'Cmdft':
        from ase.io.cmdft import read_I_info
        return read_I_info(filename)

    if format == 'tmol':
        from ase.io.turbomole import read_turbomole
        return read_turbomole(filename)

    if format == 'tmol-gradient':
        from ase.io.turbomole import read_turbomole_gradient
        return read_turbomole_gradient(filename)

    if format == 'cfg':
        from ase.io.cfg import read_cfg
        return read_cfg(filename)

    if format == 'dftb':
        from ase.io.dftb import read_dftb
        return read_dftb(filename)

    if format == 'sdf':
        from ase.io.sdf import read_sdf
        return read_sdf(filename)

    if format == 'etsf':
        from ase.io.etsf import ETSFReader
        return ETSFReader(filename).read_atoms()

    if format == 'gen':
        from ase.io.gen import read_gen
        return read_gen(filename)

    if format == 'cmr':
        from ase.io.cmr_io import read_db
        return read_db(filename, index)

    if format == 'lammps':
        from ase.io.lammpsrun import read_lammps_dump
        return read_lammps_dump(filename, index)

    if format == 'eon':
        from ase.io.eon import read_reactant_con
        return read_reactant_con(filename)

    if format == 'gromacs':
        from ase.io.gromacs import read_gromacs
        return read_gromacs(filename)

    if format == 'gaussian':
        from ase.io.gaussian import read_gaussian
        return read_gaussian(filename)

    if format == 'gaussian_out':
        from ase.io.gaussian import read_gaussian_out
        return read_gaussian_out(filename, index)

    if format == 'esp_in':
        from ase.io.espresso import read_espresso_in
        return read_espresso_in(filename)

    if format == 'esp_out':
        from ase.io.espresso import read_espresso_out
        return read_espresso_out(filename, index)

    if format == 'nw':
        from ase.io.nwchem import read_nwchem_input
        return read_nwchem_input(filename)

    if format == 'xsd':
        from ase.io.xsd import read_xsd
        return read_xsd(filename)

    raise RuntimeError('File format descriptor ' + format + ' not recognized!')
Exemple #3
0
def read(filename, index=-1, format=None):
    """Read Atoms object(s) from file.

    filename: str
        Name of the file to read from.
    index: int or slice
        If the file contains several configurations, the last configuration
        will be returned by default.  Use index=n to get configuration
        number n (counting from zero).
    format: str
        Used to specify the file-format.  If not given, the
        file-format will be guessed by the *filetype* function. If
        it's 'babel', will try to use the OpenBabel library.

    Known formats:

    =========================  ===========
    format                     short name
    =========================  ===========
    GPAW restart-file          gpw
    Dacapo netCDF output file  dacapo
    Old ASE netCDF trajectory  nc
    Virtual Nano Lab file      vnl
    ASE pickle trajectory      traj
    GPAW text output           gpaw-text
    CUBE file                  cube
    XCrySDen Structure File    xsf  
    Dacapo text output         dacapo-text
    XYZ-file                   xyz
    VASP POSCAR/CONTCAR file   vasp
    Protein Data Bank          pdb
    VTK XML Image Data         vti
    VTK XML Structured Grid    vts
    VTK XML Unstructured Grid  vtu
    =========================  ===========

    """
    p = filename.rfind('@')
    if p != -1:
        try:
            index = string2index(filename[p + 1:])
        except ValueError:
            pass
        else:
            filename = filename[:p]

    if format is None:
        format = filetype(filename)

    if format.startswith('gpw'):
        import gpaw
        r = gpaw.io.open(filename, 'r')
        positions = r.get('CartesianPositions') * Bohr
        numbers = r.get('AtomicNumbers')
        cell = r.get('UnitCell') * Bohr
        pbc = r.get('BoundaryConditions')
        tags = r.get('Tags')
        magmoms = r.get('MagneticMoments')

        atoms = Atoms(positions=positions,
                      numbers=numbers,
                      cell=cell,
                      pbc=pbc)
        if tags.any():
            atoms.set_tags(tags)
        if magmoms.any():
            atoms.set_initial_magnetic_moments(magmoms)

        return atoms

    if format == 'xyz':
        from ase.io.xyz import read_xyz
        return read_xyz(filename, index)

    if format == 'traj':
        from ase.io.trajectory import read_trajectory
        return read_trajectory(filename, index)

    if format == 'cube':
        from ase.io.cube import read_cube
        return read_cube(filename, index)

    if format == 'nc':
        from ase.io.netcdf import read_netcdf
        return read_netcdf(filename, index)

    if format == 'gpaw-text':
        from ase.io.gpawtext import read_gpaw_text
        return read_gpaw_text(filename, index)

    if format == 'dacapo-text':
        from ase.io.dacapo import read_dacapo_text
        return read_dacapo_text(filename)

    if format == 'dacapo':
        from ase.io.dacapo import read_dacapo
        return read_dacapo(filename)
    
    if format == 'xsf':
        from ase.io.xsf import read_xsf
        return read_xsf(filename, index)

    if format == 'vasp':
        from ase.io.vasp import read_vasp
        return read_vasp(filename)
    
    if format == 'mol':
        from ase.io.mol import read_mol
        return read_mol(filename)

    if format == 'pdb':
        from ase.io.pdb import read_pdb
        return read_pdb(filename)

    if format == 'cif':
        from ase.io.cif import read_cif
        return read_cif(filename)

    if format == 'babel':
        from ase.io.babel import read_babel
        return read_babel(filename, index=index)

    if format == 'vti':
        from ase.io.vtkxml import read_vti
        return read_vti(filename)

    if format == 'vts':
        from ase.io.vtkxml import read_vts
        return read_vts(filename)

    if format == 'vtu':
        from ase.io.vtkxml import read_vtu
        return read_vtu(filename)

    if format == 'iwm':
        from ase.io.iwm import read_iwm
        return read_iwm(filename)

    if format == 'Cmdft':
        from ase.io.cmdft import read_I_info
        return read_I_info(filename)

    raise RuntimeError('That can *not* happen!')