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# Source code for ase.io.exciting

    """
    This is the implementation of the exciting I/O functions
    The functions are called with read write using the format "exciting"

    """

    import numpy as np
    import xml.etree.ElementTree as ET
    from ase.atoms import Atoms
    from ase.units import Bohr
    from xml.dom import  minidom

    def read_exciting(fileobj, index=-1):
        """Reads structure from exiting xml file.

        Parameters
        ----------
        fileobj: file object
            File handle from which data should be read.

        Other parameters
        ----------------
        index: integer -1
            Not used in this implementation.
        """

        # 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)
        # scale unit cell accorting to scaling attributes
        if 'scale' in doc.find('structure/crystal').attrib:
            scale = float(str(doc.find('structure/crystal').attrib['scale']))
        else:
            scale = 1

        if 'stretch' in doc.find('structure/crystal').attrib:
            a, b, c = doc.find('structure/crystal').attrib['stretch'].text.split()
            stretch = np.array([float(a), float(b), float(c)])
        else:
            stretch = np.array([1.0, 1.0, 1.0])
        basevectsn = root.findall('structure/crystal/basevect')
        for basevect in basevectsn:
            x, y, z = basevect.text.split()
            basevects.append(np.array([float(x) * Bohr * stretch[0],
                                       float(y) * Bohr * stretch[1],
                                       float(z) * Bohr * stretch[2]
                                       ]) * scale)
        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(filename, images):
        """writes exciting input structure in XML

        Parameters
        ----------
        filename : str
            Name of file 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
        -------
        """
        fileobj = open(filename, 'wb')
        root = atoms2etree(images)
        rough_string = ET.tostring(root, 'utf-8')
        reparsed = minidom.parseString(rough_string)
        pretty = reparsed.toprettyxml(indent="\t")
        fileobj.write(pretty.encode('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

        Returns
        -------
        root : etree object
            Element tree of exciting input file containing the structure
        """
        if not isinstance(images, (list, tuple)):
            images = [images]

        root = ET.Element('input')
        root.set(
            '{http://www.w3.org/2001/XMLSchema-instance}noNamespaceSchemaLocation',
            'http://xml.exciting-code.org/excitinginput.xsd')

        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)

        oldsymbol = ''
        oldrmt = -1
        newrmt = -1
        scaled = atoms.get_scaled_positions()
        for aindex, symbol in enumerate(atoms.get_chemical_symbols()):
            if 'rmt' in atoms.arrays:
                newrmt = atoms.get_array('rmt')[aindex] / Bohr
            if symbol != oldsymbol or newrmt != oldrmt:
                speciesnode = ET.SubElement(structure, 'species',
                                            speciesfile='%s.xml' % symbol,
                                            chemicalSymbol=symbol)
                oldsymbol = symbol
                if 'rmt' in atoms.arrays:
                    oldrmt = atoms.get_array('rmt')[aindex] / Bohr
                    if oldrmt > 0:
                        speciesnode.attrib['rmt'] = '%.4f' % oldrmt

            atom = ET.SubElement(speciesnode, 'atom',
                                 coord='%.14f %.14f %.14f' % tuple(scaled[aindex]))
            if 'momenta' in atoms.arrays:
                atom.attrib['bfcmt'] = '%.14f %.14f %.14f' % tuple(
                    atoms.get_array('mommenta')[aindex])

        return root

Documentation v: 3.19.0

Versions
  3.20.0b1 (development)
  3.19.0 (latest stable)