def _get_atoms(filename, topology, unit_style, type_list):
"""Function to parse the atom information in the LAMMPS data file
"""
with open(filename, 'r') as lammps_file:
for i, line in enumerate(lammps_file):
if 'atoms' in line.split():
n_atoms = int(line.split()[0])
if 'Atoms' in line.split():
break
atom_lines = open(filename, 'r').readlines()[i+2:i+n_atoms+2]
for line in atom_lines:
atom_line = line.split()
atom_type = atom_line[2]
charge = u.unyt_quantity(float(atom_line[3]), get_units(unit_style)['charge'])
coord = u.angstrom * u.unyt_array([
float(atom_line[4]),
float(atom_line[5]),
float(atom_line[6])])
site = Site(
charge=charge,
position=coord,
atom_type=type_list[int(atom_type)-1]
)
element = element_by_mass(site.atom_type.mass.value)
site.name = element.name
site.element = element
topology.add_site(site)
topology.update_sites()
return topology
def test_setters_and_getters(self):
site = Site(name='Lithium', element=Lithium, charge=1, mass=6.941)
assert site.name == 'Lithium'
assert site.element == Lithium
assert site.charge == 1 * u.elementary_charge
assert site.mass == 6.941 * u.gram / u.mol
site.name = 'Sulfur'
site.element = Sulfur
site.charge = -1
site.mass = 32.065
assert site.name == 'Sulfur'
assert site.element == Sulfur
assert site.charge == -1 * u.elementary_charge
assert site.mass == 32.065 * u.gram / u.mol
site.element, site.charge, site.mass = None, None, None
assert site.element is None
assert site.charge is None
assert site.mass is None
