def get_structuredata_ncf(self):
"""
This routine returns an AiiDA Structure Data type produced from the ``inp.xml``
file. not a calcfunction
:param self: a FleurinpData instance to be parsed into a StructureData
:returns: StructureData node, or None
"""
from aiida.orm import StructureData
from masci_tools.util.xml.xml_getters import get_structure_data
xmltree, schema_dict = self.load_inpxml()
atoms, cell, pbc = get_structure_data(xmltree,
schema_dict,
site_namedtuple=True)
struc = StructureData(cell=cell, pbc=pbc)
for atom in atoms:
struc.append_atom(position=atom.position,
symbols=atom.symbol,
name=atom.kind)
# TODO DATA-DATA links are not wanted, you might want to use a cf instead
#struc.add_link_from(self, label='self.structure', link_type=LinkType.CREATE)
# label='self.structure'
# return {label : struc}
return struc
def test_get_structure_max4(load_inpxml, data_regression):
from masci_tools.util.xml.xml_getters import get_structure_data
from masci_tools.io.common_functions import convert_to_pystd
xmltree, schema_dict = load_inpxml(TEST_MAX4_INPXML_PATH)
atoms, cell, pbc = get_structure_data(xmltree, schema_dict)
data_regression.check({
'atoms': convert_to_pystd(atoms),
'cell': convert_to_pystd(cell),
'pbc': pbc
})
def test_get_structure_data(load_inpxml, inpxmlfilepath):
"""
Test that get_cell works for all input files
"""
from masci_tools.util.xml.xml_getters import get_structure_data
import numpy as np
xmltree, schema_dict = load_inpxml(inpxmlfilepath)
atoms, cell, pbc = get_structure_data(xmltree, schema_dict)
assert isinstance(atoms, list)
assert len(atoms) != 0
assert isinstance(cell, np.ndarray)
assert cell.shape == (3, 3)
assert isinstance(pbc, list)
assert len(pbc) == 3