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_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_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_write_lammps(self, topology_site):
top = topology_site()
write_lammpsdata(top, filename='data.lammps')
def test_write_lammps_triclinic(self, topology_site):
top = topology_site()
top.box = Box(lengths=[1,1,1], angles=[60,90,120])
write_lammpsdata(top, filename='data.triclinic')
def test_write_lammps(self, typed_ar_system):
write_lammpsdata(typed_ar_system, filename='data.lammps')
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_water_lammps(self, typed_water_system):
write_lammpsdata(typed_water_system, 'data.water')
def test_write_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')
def test_ethane_lammps(self, typed_ethane):
write_lammpsdata(typed_ethane, 'data.ethane')
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
