"""
Sile object for reading/writing XV files
"""
from __future__ import print_function
import numpy as np
# Import sile objects
from .sile import SileSiesta
from ..sile import *
# Import the geometry object
from sisl import Geometry, Atom, SuperCell
from sisl.units.siesta import unit_convert
Bohr2Ang = unit_convert('Bohr', 'Ang')
__all__ = ['XVSileSiesta']
[docs]class XVSileSiesta(SileSiesta):
""" XV file object """
def _setup(self):
""" Setup the `XVSileSiesta` after initialization """
self._comment = []
@Sile_fh_open
def write_geometry(self, geom, fmt='.8f'):
""" Writes the geometry to the contained file """
# Check that we can write to the file
sile_raise_write(self)
# Write unit-cell
tmp = np.zeros(6, np.float64)
# Create format string for the cell-parameters
fmt_str = (' ' + ('{:' + fmt + '} ') * 3) * 2 + '\n'
for i in range(3):
tmp[0:3] = geom.cell[i, :] / Bohr2Ang
self._write(fmt_str.format(*tmp))
self._write('{:12d}\n'.format(geom.na))
# Create format string for the atomic coordinates
fmt_str = '{:3d}{:4d} '
fmt_str += ('{:' + fmt + '} ') * 3 + ' '
fmt_str += ('{:' + fmt + '} ') * 3 + '\n'
for ia, a, ips in geom.iter_species():
tmp[0:3] = geom.xyz[ia, :] / Bohr2Ang
self._write(fmt_str.format(ips + 1, a.Z, *tmp))
@Sile_fh_open
def read_supercell(self):
""" Returns `SuperCell` object from the XV file """
cell = np.empty([3, 3], np.float64)
for i in range(3):
cell[i, :] = list(map(float, self.readline().split()[:3]))
cell *= Bohr2Ang
return SuperCell(cell)
@Sile_fh_open
def read_geometry(self):
""" Returns Geometry object from the XV file
"""
sc = self.read_supercell()
# Read number of atoms
na = int(self.readline())
atms = [None] * na
xyz = np.empty([na, 3], np.float64)
line = np.empty(8, np.float64)
for ia in range(na):
line[:] = list(map(float, self.readline().split()[:8]))
atms[ia] = Atom[int(line[1])]
xyz[ia, :] = line[2:5]
xyz *= Bohr2Ang
return Geometry(xyz, atms, sc=sc)
[docs] def ArgumentParser(self, *args, **kwargs):
""" Returns the arguments that is available for this Sile """
newkw = Geometry._ArgumentParser_args_single()
newkw.update(kwargs)
return self.read_geometry().ArgumentParser(*args, **newkw)
add_sile('XV', XVSileSiesta, gzip=True)