Chimie Théorique » QMX

"""

This is the Implementation of the exciting I/O Functions

The functions are called with read write usunf the format "exi"

The module depends on lxml  http://codespeak.net/lxml/

"""

from math import pi, cos, sin, sqrt, acos

from ase.atoms import Atoms

from ase.parallel import paropen

from ase.units import Bohr

def read_exciting(fileobj, index=-1):

    """Reads structure from exiting xml file.

    Parameters

    ----------

    fileobj: file object

        Filehandle from which data should be read.

    Other parameters

    ----------------

    index: integer -1

        Not used in this implementation.

    """

    from lxml import etree as ET

    #parse file into element tree

    doc = ET.parse(fileobj)

    root = doc.getroot()

    speciesnodes = root.find('structure').getiterator('species')

    symbols = []

    positions = []

    basevects = []

    atoms = None

    #collect data from tree

    for speciesnode in speciesnodes:

        symbol = speciesnode.get('speciesfile').split('.')[0]

        natoms = speciesnode.getiterator('atom')

        for atom in natoms:

            x, y, z = atom.get('coord').split()

            positions.append([float(x), float(y), float(z)])

            symbols.append(symbol)

    basevectsn = doc.xpath('//basevect/text()')

    for basevect in basevectsn:

        x, y, z = basevect.split()

        basevects.append([float(x) * Bohr, float(y) * Bohr, float(z) * Bohr])

    atoms = Atoms(symbols=symbols, cell=basevects)

    atoms.set_scaled_positions(positions)

    if 'molecule' in root.find('structure').attrib.keys():

        if root.find('structure').attrib['molecule']:

            atoms.set_pbc(False)

    else:

        atoms.set_pbc(True)

    return atoms

def write_exciting(fileobj, images):

    """writes exciting input structure in XML

    Parameters

    ----------

    fileobj : File object

        Filehandle to which data should be written

    images : Atom Object or List of Atoms objects

        This function will write the first Atoms object to file

    Returns

    -------

    """

    from lxml import etree as ET

    if isinstance(fileobj, str):

        fileobj = paropen(fileobj, 'w')

    root = atoms2etree(images)

    fileobj.write(ET.tostring(root, method='xml',

                              pretty_print=True,

                              xml_declaration=True,

                              encoding='UTF-8'))

def atoms2etree(images):

    """This function creates the xml DOM corresponding

     to the structure for use in write and calculator

    Parameters

    ----------

    images : Atom Object or List of Atoms objects

        This function will create a

    Returns

    -------

    root : etree object

        Element tree of exciting input file containing the structure

    """

    from lxml import etree as ET

    if not isinstance(images, (list, tuple)):

        images = [images]

    root = ET.Element('input')

    title = ET.SubElement(root, 'title')

    title.text = ''

    structure = ET.SubElement(root, 'structure')

    crystal= ET.SubElement(structure, 'crystal')

    atoms = images[0]

    for vec in atoms.cell:

        basevect = ET.SubElement(crystal, 'basevect')

        basevect.text = '%.14f %.14f %.14f' % tuple(vec / Bohr)

    species = {}

    symbols = []

    for a, symbol in enumerate(atoms.get_chemical_symbols()):

        if symbol in species:

            species[symbol].append(a)

        else:

            species[symbol] = [a]

            symbols.append(symbol)

    scaled = atoms.get_scaled_positions()

    for symbol in symbols:

        speciesnode = ET.SubElement(structure, 'species',

                                    speciesfile='%s.xml' % symbol,

                                    chemicalSymbol=symbol)

        for a in species[symbol]:

           atom = ET.SubElement(speciesnode, 'atom',

                                coord='%.14f %.14f %.14f' % tuple(scaled[a]))

    return root