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
