# 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/.
from __future__ import annotations
import numpy as np
from sisl import Atom, AtomGhost, Atoms, Geometry, Lattice
from sisl._internal import set_module
from sisl.messages import deprecate_argument
from sisl.unit.siesta import unit_convert
from .._help import _fill_basis_empty
from ..sile import add_sile, sile_fh_open, sile_raise_write
from .sile import SileSiesta
__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: Geometry, fmt: str = ".9f"):
"""Writes the geometry to the contained file
Parameters
----------
geometry :
geometry to write in the STRUCT file
fmt :
the precision used for writing the coordinates in the 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_lattice(self) -> Lattice:
"""Returns `Lattice` 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 Lattice(cell)
[docs]
@sile_fh_open()
@deprecate_argument(
"species_Z",
"species_as_Z",
"use species_as_Z= instead of species_Z=",
"0.15",
"0.17",
)
@deprecate_argument(
"species_as_Z",
None,
"species_as_Z= is deprecated, please pass an Atoms object with the basis information as atoms=",
"0.15",
"0.17",
)
def read_geometry(
self, atoms: Optional[Atoms, Geometry] = None, species_as_Z: bool = False
) -> Geometry:
"""Returns a `Geometry` object from the ``STRUCT`` file
Parameters
----------
atoms :
an object containing the basis information, is useful to overwrite
the atoms object contained in the geometry.
species_as_Z :
Deprecated, it does nothing!
Returns
-------
Geometry
"""
lattice = self.read_lattice()
# 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])
Z = int(line[1])
atms[ia] = Atom(Z)
xyz[ia, :] = line[2:5]
xyz = xyz @ lattice.cell
if atoms is None:
atoms = atms
# Ensure correct sorting
atms2 = _fill_basis_empty(sp - 1, atoms)
return Geometry(xyz, atms2, lattice=lattice)
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)