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# Source code for ase.io.siesta

    """Helper functions for read_fdf."""
    from os import fstat
    from re import compile
    from ase.utils import reader

    _label_strip_re = compile(r'[\s._-]')

    def _labelize(raw_label):
        # Labels are case insensitive and -_. should be ignored, lower and strip it
        return _label_strip_re.sub('', raw_label).lower()

    def _is_block(val):
        # Tell whether value is a block-value or an ordinary value.
        # A block is represented as a list of lists of strings,
        # and a ordinary value is represented as a list of strings
        if isinstance(val, list) and \
           len(val) > 0 and \
           isinstance(val[0], list):
            return True
        return False

    def _get_stripped_lines(fd):
        # Remove comments, leading blanks, and empty lines
        return [_f for _f in [L.split('#')[0].strip() for L in fd] if _f]

    @reader
    def _read_fdf_lines(file, inodes=[]):
        # Read lines and resolve includes
        fst = fstat(file.fileno())
        inode = (fst.st_dev, fst.st_ino)
        if inode in inodes:
            raise IOError('Cyclic include in fdf file')
        inodes = inodes + [inode]

        lbz = _labelize

        lines = []
        for L in _get_stripped_lines(file):
            w0 = lbz(L.split(None, 1)[0])

            if w0 == '%include':
                # Include the contents of fname
                fname = L.split(None, 1)[1].strip()
                lines += _read_fdf_lines(fname, inodes)

            elif '<' in L:
                L, fname = L.split('<', 1)
                w = L.split()
                fname = fname.strip()

                if w0 == '%block':
                    # "%block label < filename" means that the block contents
                    # should be read from filename
                    if len(w) != 2:
                        raise IOError('Bad %%block-statement "%s < %s"' %
                                      (L, fname))
                    label = lbz(w[1])
                    lines.append('%%block %s' % label)
                    lines += _get_stripped_lines(open(fname))
                    lines.append('%%endblock %s' % label)
                else:
                    # "label < filename.fdf" means that the label
                    # (_only_ that label) is to be resolved from filename.fdf
                    label = lbz(w[0])
                    fdf = _read_fdf(fname, inodes)
                    if label in fdf:
                        if _is_block(fdf[label]):
                            lines.append('%%block %s' % label)
                            lines += [' '.join(x) for x in fdf[label]]
                            lines.append('%%endblock %s' % label)
                        else:
                            lines.append('%s %s' % (label, ' '.join(fdf[label])))
                    # else:
                    #    label unresolved!
                    #    One should possibly issue a warning about this!
            else:
                # Simple include line L
                lines.append(L)
        return lines

    # The reason for creating a separate _read_fdf is simply to hide the
    # inodes-argument
    def _read_fdf(fname, inodes=[]):
        # inodes is used to detect cyclic includes
        fdf = {}
        lbz = _labelize
        lines = _read_fdf_lines(fname, inodes)
        while lines:
            w = lines.pop(0).split(None, 1)
            if lbz(w[0]) == '%block':
                # Block value
                if len(w) == 2:
                    label = lbz(w[1])
                    content = []
                    while True:
                        if len(lines) == 0:
                            raise IOError('Unexpected EOF reached in %s, '
                                          'un-ended block %s' % (fname, label))
                        w = lines.pop(0).split()
                        if lbz(w[0]) == '%endblock':
                            break
                        content.append(w)

                    if label not in fdf:
                        # Only first appearance of label is to be used
                        fdf[label] = content
                else:
                    raise IOError('%%block statement without label')
            else:
                # Ordinary value
                label = lbz(w[0])
                if len(w) == 1:
                    # Siesta interpret blanks as True for logical variables
                    fdf[label] = []
                else:
                    fdf[label] = w[1].split()
        return fdf

    def read_fdf(fname):
        """Read a siesta style fdf-file.

        The data is returned as a dictionary
        ( label:value ).

        All labels are converted to lower case characters and
        are stripped of any '-', '_', or '.'.

        Ordinary values are stored as a list of strings (splitted on WS),
        and block values are stored as list of lists of strings
        (splitted per line, and on WS).
        If a label occurres more than once, the first occurrence
        takes precedence.

        The implementation applies no intelligence, and does not
        "understand" the data or the concept of units etc.
        Values are never parsed in any way, just stored as
        split strings.

        The implementation tries to comply with the fdf-format
        specification as presented in the siesta 2.0.2 manual.

        An fdf-dictionary could e.g. look like this::

            {'atomiccoordinatesandatomicspecies': [
                  ['4.9999998', '5.7632392', '5.6095972', '1'],
                  ['5.0000000', '6.5518100', '4.9929091', '2'],
                  ['5.0000000', '4.9746683', '4.9929095', '2']],
             'atomiccoordinatesformat': ['Ang'],
             'chemicalspecieslabel': [['1', '8', 'O'],
                                      ['2', '1', 'H']],
             'dmmixingweight': ['0.1'],
             'dmnumberpulay': ['5'],
             'dmusesavedm': ['True'],
             'latticeconstant': ['1.000000', 'Ang'],
             'latticevectors': [
                  ['10.00000000', '0.00000000', '0.00000000'],
                  ['0.00000000', '11.52647800', '0.00000000'],
                  ['0.00000000', '0.00000000', '10.59630900']],
             'maxscfiterations': ['120'],
             'meshcutoff': ['2721.139566', 'eV'],
             'numberofatoms': ['3'],
             'numberofspecies': ['2'],
             'paobasissize': ['dz'],
             'solutionmethod': ['diagon'],
             'systemlabel': ['H2O'],
             'wavefunckpoints': [['0.0', '0.0', '0.0']],
             'writedenchar': ['T'],
             'xcauthors': ['PBE'],
             'xcfunctional': ['GGA']}

        """

        return _read_fdf(fname)

    def read_struct_out(fname):
        """Read a siesta struct file"""
        from ase.atoms import Atoms, Atom

        f = fname

        cell = []
        for i in range(3):
            cell.append([float(x) for x in f.readline().split()])

        natoms = int(f.readline())

        atoms = Atoms()
        for atom in f:
            Z, pos_x, pos_y, pos_z = atom.split()[1:]
            atoms.append(Atom(int(Z),
                              position=(float(pos_x), float(pos_y), float(pos_z))))

        if len(atoms) != natoms:
            raise IOError('Badly structured input file')

        atoms.set_cell(cell, scale_atoms=True)

        return atoms

Documentation v: 3.19.0

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  3.19.0 (latest stable)