def test_read_sigma(self, filename=get_path('data.lammps')): read = read_lammpsdata(filename) lj = [i.parameters for i in read.atom_types][0] assert_allclose_units(lj['sigma'], u.unyt_array(3, u.angstrom), rtol=1e-5, atol=1e-8)
def test_read_epsilon(self, filename=get_path('data.lammps')): read = read_lammpsdata(filename) lj = [i.parameters for i in read.atom_types][0] assert_allclose_units(lj['epsilon'], u.unyt_array(0.0717, (u.kcal / u.mol)), rtol=1e-5, atol=1e-8)
def test_read_mass(self, filename=get_path('data.lammps')): read = read_lammpsdata(filename) masses = [i.mass for i in read.atom_types] assert_allclose_units(masses, u.unyt_array(1.0079, u.g), rtol=1e-5, atol=1e-8)
def test_read_charge(self, filename=get_path('data.lammps')): read = read_lammpsdata(filename) charge = [i.charge for i in read.atom_types] assert_allclose_units(charge, u.unyt_array(0, u.C), rtol=1e-5, atol=1e-8)
def test_read_lammps_triclinic(self, typed_ar_system): typed_ar_system.box = Box(lengths=[1,1,1], angles=[60,90,120]) write_lammpsdata(typed_ar_system, filename='data.triclinic') read = read_lammpsdata('data.triclinic') assert u.array.allclose_units(read.box.lengths, u.unyt_array([1,1,1], u.nm)) assert u.array.allclose_units(read.box.angles, u.unyt_array([60, 90, 120], u.degree))
def test_read_water(self, typed_water_system): write_lammpsdata(typed_water_system, filename='data.water') water = read_lammpsdata('data.water') assert u.array.allclose_units(water.sites[0].charge, u.unyt_array(-0.834, u.elementary_charge)) assert water.n_sites == 6 assert water.n_connections == 6
def test_read_water(self, typed_water_system): write_lammpsdata(typed_water_system, filename="data.water") water = read_lammpsdata("data.water") assert_allclose_units( water.sites[0].charge, u.unyt_array(-0.834, u.elementary_charge), rtol=1e-5, atol=1e-8, ) assert water.n_sites == 6 assert water.n_connections == 6
def test_read_lammps_triclinic(self, typed_ar_system): typed_ar_system.box = Box(lengths=[1, 1, 1], angles=[60, 90, 120]) write_lammpsdata(typed_ar_system, filename="data.triclinic") read = read_lammpsdata("data.triclinic") assert_allclose_units( read.box.lengths, u.unyt_array([1, 1, 1], u.nm), rtol=1e-5, atol=1e-8, ) assert_allclose_units( read.box.angles, u.unyt_array([60, 90, 120], u.degree), rtol=1e-5, atol=1e-8, )
def test_read_n_sites(self, typed_ar_system): write_lammpsdata(typed_ar_system, filename='data.ar') read = read_lammpsdata('data.ar') assert read.n_sites == 100
def test_read_sites(self, filename=get_path('data.lammps')): read = read_lammpsdata(filename) assert read.box == Box(lengths=[1, 1, 1])
def test_read_lammps(self, filename=get_path('data.lammps')): read_lammpsdata(filename)
def test_read_epsilon(self, filename=get_path('data.lammps')): read = read_lammpsdata(filename) lj = [i.parameters for i in read.atom_types][0] assert lj['epsilon'] == u.unyt_array(0.0717, (u.kcal/u.mol))
def test_read_sigma(self, filename=get_path('data.lammps')): read = read_lammpsdata(filename) lj = [i.parameters for i in read.atom_types][0] assert lj['sigma'] == u.unyt_array(3, u.angstrom)
def test_read_mass(self, filename=get_path('data.lammps')): read = read_lammpsdata(filename) charge = [i.charge for i in read.atom_types] assert charge == u.unyt_array(0, u.C)
def test_read_mass(self, filename=get_path('data.lammps')): read = read_lammpsdata(filename) masses = [i.mass for i in read.atom_types] assert masses == u.unyt_array(1, u.g)
def test_read_n_sites(self, topology_site): write_lammpsdata(topology_site(sites=4), filename='data.four_sites') read = read_lammpsdata('data.four_sites') assert read.n_sites == 4