def get(self, key, unit=None, default=None, with_unit=False):
""" Retrieve fdf-keyword from the file """
# First split into specification and key
key, tmp_unit = name_spec(key)
if unit is None:
unit = tmp_unit
found, fdf = self._read(key)
if not found:
return default
# The keyword is found...
if fdf.startswith('%block'):
found, fdf = self._read_block(key)
if not found:
return default
else:
return fdf
# We need to process the returned value further.
fdfl = fdf.split()
# Check whether this is a logical flag
if len(fdfl) == 1:
# This *MUST* be a boolean
# SCF.Converge.H
# defaults to .true.
return True
elif fdfl[1] in _LOGICAL_TRUE:
return True
elif fdfl[1] in _LOGICAL_FALSE:
return False
# It is something different.
# Try and figure out what it is
if len(fdfl) == 3:
# We expect it to be a unit
if unit is None:
# Get group of unit
group = unit_group(fdfl[2])
# return in default sisl units
unit = unit_default(group)
if with_unit and tmp_unit is not None:
# The user has specifically requested the unit:
# key{unit}
return '{0:.4f} {1}'.format(
float(fdfl[1]) * unit_convert(fdfl[2], unit), unit)
elif not with_unit:
return float(fdfl[1]) * unit_convert(fdfl[2], unit)
return ' '.join(fdfl[1:])
def get(self, key, unit=None, default=None, with_unit=False):
""" Retrieve fdf-keyword from the file """
# First split into specification and key
key, tmp_unit = name_spec(key)
if unit is None:
unit = tmp_unit
found, fdf = self._read(key)
if not found:
return default
# The keyword is found...
if fdf.startswith('%block'):
found, fdf = self._read_block(key)
if not found:
return default
else:
return fdf
# We need to process the returned value further.
fdfl = fdf.split()
# Check whether this is a logical flag
if len(fdfl) == 1:
# This *MUST* be a boolean
# SCF.Converge.H
# defaults to .true.
return True
elif fdfl[1] in _LOGICAL_TRUE:
return True
elif fdfl[1] in _LOGICAL_FALSE:
return False
# It is something different.
# Try and figure out what it is
if len(fdfl) == 3:
# We expect it to be a unit
if unit is None:
# Get group of unit
group = unit_group(fdfl[2])
# return in default sisl units
unit = unit_default(group)
if with_unit and tmp_unit is not None:
# The user has specifically requested the unit:
# key{unit}
return '{0:.4f} {1}'.format(float(fdfl[1]) * unit_convert(fdfl[2], unit), unit)
elif not with_unit:
return float(fdfl[1]) * unit_convert(fdfl[2], unit)
return ' '.join(fdfl[1:])
# Check against integers
from numbers import Integral
# Import sile objects
from .tbtrans import tbtncSileSiesta
from ..sile import *
from sisl.utils import *
# Import the geometry object
from sisl import Geometry, Atom, SuperCell
from sisl._help import _str
from sisl.units.siesta import unit_convert
__all__ = ['tbtprojncSileSiesta', 'phtprojncSileSiesta']
Bohr2Ang = unit_convert('Bohr', 'Ang')
Ry2eV = unit_convert('Ry', 'eV')
Ry2K = unit_convert('Ry', 'K')
eV2Ry = unit_convert('eV', 'Ry')
class tbtprojncSileSiesta(tbtncSileSiesta):
""" TBtrans projection file object """
_trans_type = 'TBT.Proj'
add_sile('TBT.Proj.nc', tbtprojncSileSiesta)
# Add spin-dependent files
add_sile('TBT_DN.Proj.nc', tbtprojncSileSiesta)
add_sile('TBT_UP.Proj.nc', tbtprojncSileSiesta)
from __future__ import print_function
# Import sile objects
from .sile import SileCDFSIESTA
from ..sile import *
# Import the geometry object
from sisl import Geometry, Atom, SuperCell, Grid
from sisl.units.siesta import unit_convert
from sisl.quantity import Hamiltonian
import numpy as np
__all__ = ['ncSileSiesta']
Bohr2Ang = unit_convert('Bohr', 'Ang')
Ry2eV = unit_convert('Ry', 'eV')
class ncSileSiesta(SileCDFSIESTA):
""" SIESTA file object """
def read_sc(self):
""" Returns a SuperCell object from a SIESTA.nc file
"""
cell = np.array(self._value('cell'), np.float64)
# Yes, this is ugly, I really should implement my unit-conversion tool
cell *= Bohr2Ang
cell.shape = (3, 3)
nsc = np.array(self._value('nsc'), np.int32)
# Import sile objects
from .sile import SileCDFSIESTA
from ..sile import *
from sisl.utils import *
# Import the geometry object
from sisl import Geometry, Atom, SuperCell
from sisl._help import _str
from sisl.units.siesta import unit_convert
__all__ = ['tbtncSileSiesta', 'phtncSileSiesta']
__all__ += ['dHncSileSiesta']
Bohr2Ang = unit_convert('Bohr', 'Ang')
Ry2eV = unit_convert('Ry', 'eV')
eV2Ry = unit_convert('eV', 'Ry')
class tbtncSileSiesta(SileCDFSIESTA):
""" TBtrans file object """
_trans_type = 'TBT'
def _value_avg(self, name, tree=None, avg=False):
""" Local method for obtaining the data from the SileCDF.
This method checks how the file is access, i.e. whether
data is stored in the object or it should be read consequtively.
"""
if self._access > 0:
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']
class XVSileSiesta(SileSiesta):
""" XV file object """
def _setup(self):
""" Setup the `XVSileSiesta` after initialization """
self._comment = []
@Sile_fh_open
def write_geom(self, geom):
""" Writes the geometry to the contained file """
"""
from __future__ import print_function
import numpy as np
# Import sile objects
from .sile import SileCDFSIESTA
from ..sile import *
# Import the geometry object
from sisl import Geometry, SuperCell, Grid
from sisl.units.siesta import unit_convert
__all__ = ['gridncSileSiesta']
Bohr2Ang = unit_convert('Bohr', 'Ang')
class gridncSileSiesta(SileCDFSIESTA):
""" SIESTA Grid file object """
def read_supercell(self):
""" Returns a SuperCell object from a SIESTA.grid.nc file
"""
cell = np.array(self._value('cell'), np.float64)
# Yes, this is ugly, I really should implement my unit-conversion tool
cell *= Bohr2Ang
cell.shape = (3, 3)
return SuperCell(cell)