# 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 .sile import *
from sisl._internal import set_module
from sisl import Geometry
__all__ = ['moldenSile']
@set_module("sisl.io")
class moldenSile(Sile):
""" Molden file object """
[docs] @sile_fh_open()
def write_supercell(self, sc):
""" 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_supercell(geometry.sc)
# 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)