def _get_atoms(filename, topology, unit_style, type_list):
"""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 = Atom(
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):
atom = Atom(name="Lithium", element=Lithium, charge=1, mass=6.941)
assert atom.name == "Lithium"
assert atom.element == Lithium
assert atom.charge == 1 * u.elementary_charge
assert atom.mass == 6.941 * u.gram / u.mol
atom.name = "Sulfur"
atom.element = Sulfur
atom.charge = -1
atom.mass = 32.065
assert atom.name == "Sulfur"
assert atom.element == Sulfur
assert atom.charge == -1 * u.elementary_charge
assert atom.mass == 32.065 * u.gram / u.mol
atom.mass = None
atom.charge = None
