def _import_ase(filename, **kwargs):
"""
Imports a structure in a number of formats using the ASE routines.
"""
from os.path import abspath
from aiida.orm.data.structure import StructureData
try:
import ase.io
except ImportError:
echo.echo_critical("You have not installed the package ase. \n"
"You can install it with: pip install ase")
store = kwargs.pop('store')
view_in_ase = kwargs.pop('view')
echo.echo('importing structure from: \n {}'.format(abspath(filename)))
filepath = abspath(filename)
try:
asecell = ase.io.read(filepath)
new_structure = StructureData(ase=asecell)
if store:
new_structure.store()
if view_in_ase:
from ase.visualize import view
view(new_structure.get_ase())
echo.echo(' Succesfully imported structure {}, '
'(PK = {})'.format(new_structure.get_formula(),
new_structure.pk))
except ValueError as err:
echo.echo_critical(err)
def _import_xyz(filename, **kwargs):
"""
Imports an XYZ-file.
"""
from os.path import abspath
from aiida.orm.data.structure import StructureData
vacuum_addition = kwargs.pop('vacuum_addition')
vacuum_factor = kwargs.pop('vacuum_factor')
pbc = [bool(i) for i in kwargs.pop('pbc')]
store = kwargs.pop('store')
view_in_ase = kwargs.pop('view')
echo.echo('importing XYZ-structure from: \n {}'.format(abspath(filename)))
filepath = abspath(filename)
with open(filepath) as fobj:
xyz_txt = fobj.read()
new_structure = StructureData()
# pylint: disable=protected-access
try:
new_structure._parse_xyz(xyz_txt)
new_structure._adjust_default_cell(vacuum_addition=vacuum_addition,
vacuum_factor=vacuum_factor,
pbc=pbc)
if store:
new_structure.store()
if view_in_ase:
from ase.visualize import view
view(new_structure.get_ase())
echo.echo(' Succesfully imported structure {}, '
'(PK = {})'.format(new_structure.get_formula(),
new_structure.pk))
except ValueError as err:
echo.echo_critical(err)