def _read_supercell(self):
""" Defered routine """
f, l = self.step_to('unit_cell_cart', case=False)
if not f:
raise ValueError("The unit-cell vectors could not be found in the seed-file.")
l = self.readline()
lines = []
while not l.startswith('end'):
lines.append(l)
l = self.readline()
# Check whether the first element is a specification of the units
pos_unit = lines[0].split()
if len(pos_unit) > 2:
unit = 1.
else:
unit = unit_convert(pos_unit[0], 'Ang')
# Remove the line with the unit...
lines.pop(0)
# Create the cell
cell = np.empty([3, 3], np.float64)
for i in [0, 1, 2]:
cell[i, :] = [float(x) for x in lines[i].split()]
return SuperCell(cell * unit)
"""
from __future__ import print_function
import numpy as np
# Import sile objects
from sisl.io.sile import *
# Import the geometry object
from sisl import Geometry, Atom, SuperCell, Grid
from sisl.units import unit_convert
__all__ = ['CUBESile']
Ang2Bohr = unit_convert('Ang', 'Bohr')
class CUBESile(Sile):
""" CUBE file object """
def _setup(self):
""" Setup the `CUBESile` after initialization """
self._comment = []
@Sile_fh_open
def write_geom(
self,
geom,
size=None,
fmt='15.10e',
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')
class ASCIISileBigDFT(SileBigDFT):
""" ASCII file object for BigDFT """
def _setup(self):
""" Initialize for `ASCIISileBigDFT` """
self._comment = ['#', '!']
@Sile_fh_open
def read_geom(self):
""" Reads a supercell from the Sile """
# 1st line is arbitrary
self.readline(True)
# Read dxx, dyx, dyy
"""
from __future__ import print_function
import numpy as np
# Import sile objects
from sisl.io.sile import *
# Import the geometry object
from sisl import Geometry, Atom, SuperCell, Grid
from sisl.units import unit_convert
__all__ = ['CUBESile']
Ang2Bohr = unit_convert('Ang', 'Bohr')
class CUBESile(Sile):
""" CUBE file object """
def _setup(self):
""" Setup the `CUBESile` after initialization """
self._comment = []
@Sile_fh_open
def write_geom(
self,
geom,
size=None,
fmt='15.10e',
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')
class ASCIISileBigDFT(SileBigDFT):
""" ASCII file object for BigDFT """
def _setup(self):
""" Initialize for `ASCIISileBigDFT` """
self._comment = ['#', '!']
@Sile_fh_open
def read_geom(self):
""" Reads a supercell from the Sile """
# 1st line is arbitrary
# Import sile objects
from .sile import SileScaleUp
from .orbocc import orboccSileScaleUp
from ..sile import *
# Import the geometry object
from sisl import Geometry, Atom, SuperCell
from sisl._help import ensure_array
from sisl.units import unit_convert
import numpy as np
__all__ = ['REFSileScaleUp', 'restartSileScaleUp']
Bohr2Ang = unit_convert('Bohr', 'Ang')
Ang2Bohr = unit_convert('Ang', 'Bohr')
class REFSileScaleUp(SileScaleUp):
""" REF file object for ScaleUp """
@Sile_fh_open
def read_supercell(self):
""" Reads a supercell from the Sile """
# 1st line is number of supercells
nsc = ensure_array(map(int, self.readline().split()[:3]), np.int32)
self.readline() # natoms, nspecies
self.readline() # species
cell = ensure_array(map(float, self.readline().split()[:9]), np.float64)
# Typically ScaleUp uses very large unit-cells
