"""
Sile object for reading/writing ascii files from BigDFT
"""
from __future__ import division, print_function
# Import sile objects
from .sile import SileBigDFT
from ..sile import *
# Import the geometry object
from sisl import Geometry, Atom, SuperCell
from sisl.units import unit_convert
import numpy as np
__all__ = ['ASCIISileBigDFT']
Bohr2Ang = unit_convert('Bohr', 'Ang')
[docs]class ASCIISileBigDFT(SileBigDFT):
""" ASCII file object for BigDFT """
def _setup(self):
""" Initialize for `ASCIISileBigDFT` """
self._comment = ['#', '!']
@Sile_fh_open
def read_geometry(self):
""" Reads a supercell from the Sile """
# 1st line is arbitrary
self.readline(True)
# Read dxx, dyx, dyy
dxx, dyx, dyy = map(float, self.readline().split()[:3])
# Read dzx, dzy, dzz
dzx, dzy, dzz = map(float, self.readline().split()[:3])
# options for the ASCII format
is_frac = False
is_angdeg = False
is_bohr = False
xyz = []
spec = []
# Now we need to read through and find keywords
try:
while True:
# Read line also with comment
l = self.readline(True)
# Empty line, means EOF
if l == '':
break
# too short, continue
if len(l) < 1:
continue
# Check for keyword
if l[1:].startswith('keyword:'):
if 'reduced' in l:
is_frac = True
if 'angdeg' in l:
is_angdeg = True
if 'bohr' in l or 'atomic' in l:
is_bohr = True
continue
elif l[0] in self._comment:
# this is a comment, cycle
continue
# Read atomic coordinates
ls = l.split()
if len(ls) < 3:
continue
# The first three are the coordinates
xyz.append([float(x) for x in ls[:3]])
# The 4th is the specie, [5th is tag]
s = ls[3]
t = s
if len(ls) > 4:
t = ls[4]
spec.append(Atom(s, tag=t))
except IOError as e:
print("I/O error({0}): {1}".format(e.errno, e.strerror))
except:
pass
if is_bohr:
dxx *= Bohr2Ang
dyx *= Bohr2Ang
dyy *= Bohr2Ang
if not is_angdeg:
dzx *= Bohr2Ang
dzy *= Bohr2Ang
dzz *= Bohr2Ang
# Create the supercell
if is_angdeg:
# The input is in skewed axis
sc = SuperCell([dxx, dyx, dyy, dzx, dzy, dzz])
else:
sc = SuperCell([[dxx, 0., 0.], [dyx, dyy, 0.], [dzx, dzy, dzz]])
# Now create the geometry
xyz = np.array(xyz, np.float64)
if is_frac:
# Transform from fractional to actual
# coordinates
xyz = np.dot(xyz, sc.cell.T)
elif is_bohr:
# Not when fractional coordinates are used
# the supercell conversion takes care of
# correct unit
xyz *= Bohr2Ang
return Geometry(xyz, spec, sc=sc)
@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 out the cell
self._write('# Created by sisl\n')
# We write the cell coordinates as the cell coordinates
fmt_str = '{{:{0}}} '.format(fmt) * 3 + '\n'
self._write(
fmt_str.format(
geom.cell[0, 0], geom.cell[1, 0], geom.cell[1, 1]))
self._write(fmt_str.format(*geom.cell[2, :]))
# This also denotes
self._write('#keyword: angstroem\n')
self._write('# Geometry containing: ' + str(len(geom)) + ' atoms\n')
f1_str = '{{1:{0}}} {{2:{0}}} {{3:{0}}} {{0:2s}}\n'.format(fmt)
f2_str = '{{2:{0}}} {{3:{0}}} {{4:{0}}} {{0:2s}} {{1:s}}\n'.format(fmt)
for ia, a, isp in geom.iter_species():
if a.symbol != a.tag:
self._write(f2_str.format(a.symbol, a.tag, *geom.xyz[ia, :]))
else:
self._write(f1_str.format(a.symbol, *geom.xyz[ia, :]))
# Add a single new line
self._write('\n')
[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('ascii', ASCIISileBigDFT, case=False, gzip=True)