/usr/share/pyshared/ase/io/exciting.py is in python-ase 3.6.0.2515-1.1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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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
import numpy as np
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
File handle 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)
# scale unit cell accorting to scaling attributes
if doc.xpath('//crystal/@scale'):
scale = float(str(doc.xpath('//crystal/@scale')[0]))
else:
scale = 1
if doc.xpath('//crystal/@stretch'):
a, b, c = doc.xpath('//crystal/@scale')[0].split()
stretch = np.array([float(a),float(b),float(c)])
else:
stretch = np.array([1.0, 1.0, 1.0])
basevectsn = doc.xpath('//basevect/text()')
for basevect in basevectsn:
x, y, z = basevect.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(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 aindex, symbol in enumerate(atoms.get_chemical_symbols()):
if symbol in species:
species[symbol].append(aindex)
else:
species[symbol] = [aindex]
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
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