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