# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
import numpy as np
from ..sile import add_sile, sile_fh_open, sile_raise_write
from .sile import SileSiesta
from sisl._internal import set_module
from sisl import Geometry, Atom, AtomGhost, AtomUnknown, Atoms, SuperCell
from sisl.unit.siesta import unit_convert
__all__ = ['structSileSiesta']
Bohr2Ang = unit_convert('Bohr', 'Ang')
@set_module("sisl.io.siesta")
class structSileSiesta(SileSiesta):
""" Geometry file """
[docs] @sile_fh_open()
def write_geometry(self, geometry, fmt='.9f'):
""" Writes the geometry to the contained file
Parameters
----------
geometry : Geometry
geometry to write in the XV file
fmt : str, optional
the precision used for writing the XV file
"""
# Check that we can write to the file
sile_raise_write(self)
# Create format string for the cell-parameters
fmt_str = ' ' + ('{:' + fmt + '} ') * 3 + '\n'
for i in range(3):
self._write(fmt_str.format(*geometry.cell[i]))
self._write(f'{geometry.na:12d}\n')
# Create format string for the atomic coordinates
fxyz = geometry.fxyz
fmt_str = '{:3d}{:6d} '
fmt_str += ('{:' + fmt + '} ') * 3 + '\n'
for ia, a, ips in geometry.iter_species():
if isinstance(a, AtomGhost):
self._write(fmt_str.format(ips + 1, -a.Z, *fxyz[ia]))
else:
self._write(fmt_str.format(ips + 1, a.Z, *fxyz[ia]))
[docs] @sile_fh_open()
def read_supercell(self):
""" Returns `SuperCell` object from the STRUCT file """
cell = np.empty([3, 3], np.float64)
for i in range(3):
cell[i, :] = list(map(float, self.readline().split()[:3]))
return SuperCell(cell)
[docs] @sile_fh_open()
def read_geometry(self, species_Z=False):
""" Returns a `Geometry` object from the STRUCT file
Parameters
----------
species_Z : bool, optional
if ``True`` the atomic numbers are the species indices (useful when
reading the ChemicalSpeciesLabel block simultaneously).
Returns
-------
Geometry
"""
sc = self.read_supercell()
# Read number of atoms
na = int(self.readline())
xyz = np.empty([na, 3], np.float64)
atms = [None] * na
sp = np.empty([na], np.int32)
for ia in range(na):
line = self.readline().split()
sp[ia] = int(line[0])
if species_Z:
atms[ia] = Atom(sp[ia])
else:
atms[ia] = Atom(int(line[1]))
xyz[ia, :] = line[2:5]
xyz = xyz @ sc.cell
# Ensure correct sorting
max_s = sp.max()
sp -= 1
# Ensure we can remove the atom after having aligned them
atms2 = Atoms(AtomUnknown(1000), na=na)
for i in range(max_s):
idx = (sp[:] == i).nonzero()[0]
if len(idx) == 0:
# Always ensure we have "something" for the unoccupied places
atms2[idx] = AtomUnknown(1000 + i)
else:
atms2[idx] = atms[idx[0]]
return Geometry(xyz, atms2.reduce(), sc=sc)
def ArgumentParser(self, p=None, *args, **kwargs):
""" Returns the arguments that is available for this Sile """
newkw = Geometry._ArgumentParser_args_single()
newkw.update(kwargs)
return self.read_geometry().ArgumentParser(p, *args, **newkw)
add_sile('STRUCT_IN', structSileSiesta, gzip=True)
add_sile('STRUCT_NEXT_ITER', structSileSiesta, gzip=True)
add_sile('STRUCT_OUT', structSileSiesta, gzip=True)