def test_parse_poscar_silly_write(fresh_aiida_env, vasp_structure, tmpdir):
"""
Parse (read, write) a reference POSCAR with silly elemental names.
Using the PoscarParser and compare the result to a reference structure.
"""
parser = PoscarParser(data=vasp_structure)
result = parser.get_quantity('poscar-structure', {})
names = result['poscar-structure'].get_site_kindnames()
assert names == ['Hamburger', 'Pizza']
symbols = result['poscar-structure'].get_symbols_set()
assert symbols == set(['As', 'In'])
temp_file = str(tmpdir.join('POSCAR'))
parser.write(temp_file)
parser = PoscarParser(file_path=temp_file)
result_reparse = parser.structure
names = result_reparse.get_site_kindnames()
assert names == ['Hamburger', 'Pizza']
symbols = result_reparse.get_symbols_set()
assert symbols == set(['X', 'X'])
def write_poscar(self, dst): # pylint: disable=unused-argument
"""
Write the POSCAR.
Passes the structures node (StructureData) to the POSCAR parser for
preparation and writes to dst.
:param dst: absolute path of the file to write to
"""
settings = self.inputs.get('settings')
settings = settings.get_dict() if settings else {}
poscar_precision = settings.get('poscar_precision', 10)
poscar_parser = PoscarParser(data=self._structure(),
precision=poscar_precision)
poscar_parser.write(dst)
def test_parse_poscar_reparse(fresh_aiida_env, vasp_structure, tmpdir):
"""
Parse (read) a reference POSCAR file.
Using the PoscarParser, parse(write), parse (read), and compare
to reference structure.
"""
path = data_path('poscar', 'POSCAR')
parser = PoscarParser(file_path=path)
temp_file = str(tmpdir.join('POSCAR'))
parser.write(temp_file)
parser = PoscarParser(file_path=temp_file)
result = parser.structure
structure = vasp_structure
assert result.cell == structure.cell
assert result.get_site_kindnames() == structure.get_site_kindnames()
assert result.sites[2].position == structure.sites[2].position
def test_parse_poscar_undercase(fresh_aiida_env, vasp_structure, tmpdir):
"""
Parse a reference POSCAR.
With potential elemental names using the PoscarParser and compare
the result to a reference structure.
"""
parser = PoscarParser(data=vasp_structure)
result = parser.get_quantity('poscar-structure', {})
names = result['poscar-structure'].get_site_kindnames()
assert names == ['In', 'As', 'As', 'In_d', 'In_d', 'As']
symbols = result['poscar-structure'].get_symbols_set()
assert symbols == set(['As', 'In'])
temp_file = str(tmpdir.join('POSCAR'))
parser.write(temp_file)
parser = PoscarParser(file_path=temp_file)
result_reparse = parser.structure
names = result_reparse.get_site_kindnames()
assert names == ['In', 'As', 'As', 'In_d', 'In_d', 'As']
symbols = result_reparse.get_symbols_set()
assert symbols == set(['As', 'In'])