# 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 sile objects
from __future__ import annotations
from sisl import Geometry
from sisl._internal import set_module
from sisl.messages import deprecate_argument
from .sile import *
__all__ = ["moldenSile"]
@set_module("sisl.io")
class moldenSile(Sile):
"""Molden file object"""
[docs]
@sile_fh_open()
@deprecate_argument("sc", "lattice", "use lattice= instead of sc=", "0.15", "0.16")
def write_lattice(self, lattice):
"""Writes the supercell to the contained file"""
# Check that we can write to the file
sile_raise_write(self)
# Write the number of atoms in the geometry
self._write("[Molden Format]\n")
# Sadly, MOLDEN does not read this information...
[docs]
@sile_fh_open()
def write_geometry(self, geometry, fmt=".8f"):
"""Writes the geometry to the contained file"""
# Check that we can write to the file
sile_raise_write(self)
# Be sure to write the supercell
self.write_lattice(geometry.lattice)
# Write in ATOM mode
self._write("[Atoms] Angs\n")
# Write out the cell information in the comment field
# This contains the cell vectors in a single vector (3 + 3 + 3)
# quantities, plus the number of supercells (3 ints)
fmt_str = (
"{{0:2s}} {{1:4d}} {{2:4d}} {{3:{0}}} {{4:{0}}} {{5:{0}}}\n".format(fmt)
)
for ia, a, _ in geometry.iter_species():
self._write(fmt_str.format(a.symbol, ia, a.Z, *geometry.xyz[ia, :]))
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("molf", moldenSile, case=False, gzip=True)