/usr/share/pyshared/ase/io/exciting.py is in python-ase 3.6.0.2515-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 | """
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
|