def test_nlist_polyethylene4_9A():
system = get_system_polyethylene4()
nlist = NeighborList(system)
rcut = 9*angstrom
nlist.request_rcut(rcut)
nlist.update()
nlist.check()
def test_nlist_polyethylene4_9A():
system = get_system_polyethylene4()
nlist = NeighborList(system)
rcut = 9 * angstrom
nlist.request_rcut(rcut)
nlist.update()
nlist.check()
def test_nlist_inc_r1():
cell = get_system_polyethylene4().cell
rmax = np.array([2])
r = np.array([0])
assert nlist_inc_r(cell, r, rmax)
assert (r == np.array([1])).all()
assert nlist_inc_r(cell, r, rmax)
assert (r == np.array([2])).all()
assert not nlist_inc_r(cell, r, rmax)
assert (r == np.array([0])).all()
def test_nlist_inc_r1():
cell = get_system_polyethylene4().cell
rmax = np.array([2])
r = np.array([0])
assert nlist_inc_r(cell, r, rmax)
assert (r == np.array([1])).all()
assert nlist_inc_r(cell, r, rmax)
assert (r == np.array([2])).all()
assert not nlist_inc_r(cell, r, rmax)
assert (r == np.array([0])).all()
def test_supercell_polyethylene_2():
system1 = get_system_polyethylene4()
system2 = system1.supercell(2)
assert abs(system2.cell.volume - system1.cell.volume * 2) < 1e-10
assert abs(system2.cell.rvecs - system1.cell.rvecs * 2).max() < 1e-10
assert system2.natom == system1.natom * 2
assert system2.nbond == system1.nbond * 2
assert abs(system2.pos[12:24] - system1.pos -
system1.cell.rvecs[0]).max() < 1e-10
assert issubclass(system2.bonds.dtype.type, np.integer)
def test_cell_polyethylene4():
cell = get_system_polyethylene4().cell
assert cell.rvecs.shape == (1, 3)
assert cell.gvecs.shape == (1, 3)
assert abs(cell.volume - np.linalg.norm(cell.rvecs[0])) < 1e-10
assert abs(np.dot(cell.gvecs, cell.rvecs.transpose()) - 1) < 1e-5
vec1 = np.array([10.0, 0.0, 105.0])*angstrom
cell.mic(vec1)
assert abs(vec1 - np.array([-0.15, -0.374, 104.89])*angstrom).max() < 1e-3
vec2 = np.array([10.0, 0.0, 105.0])*angstrom
cell.add_vec(vec2, cell.to_center(vec2))
assert abs(vec1 - vec2).max() < 1e-10
cell.add_vec(vec1, np.array([1]))
assert abs(vec1 - np.array([4.925, -0.187, 104.945])*angstrom).max() < 1e-3
def test_cell_polyethylene4():
cell = get_system_polyethylene4().cell
assert cell.rvecs.shape == (1, 3)
assert cell.gvecs.shape == (1, 3)
assert abs(cell.volume - np.linalg.norm(cell.rvecs[0])) < 1e-10
assert abs(np.dot(cell.gvecs, cell.rvecs.transpose()) - 1) < 1e-5
vec1 = np.array([10.0, 0.0, 105.0])*angstrom
cell.mic(vec1)
assert abs(vec1 - np.array([-0.15, -0.374, 104.89])*angstrom).max() < 1e-3
vec2 = np.array([10.0, 0.0, 105.0])*angstrom
cell.add_vec(vec2, cell.to_center(vec2))
assert abs(vec1 - vec2).max() < 1e-10
cell.add_vec(vec1, np.array([1]))
assert abs(vec1 - np.array([4.925, -0.187, 104.945])*angstrom).max() < 1e-3
def get_ff_polyethylene(**kwargs):
system = get_system_polyethylene4()
system = system.supercell(2)
fn_pars = context.get_fn('test/parameters_alkane.txt')
return ForceField.generate(system, fn_pars, **kwargs)
def test_vtens_pext_1():
system = get_system_polyethylene4()
part = ForcePartPressure(system, 1.0)
check_vtens_part(system, part)
def test_topology_polyethylene4():
system = get_system_polyethylene4()
check_topology_slow(system)
def test_vtens_pext_1():
system = get_system_polyethylene4()
part = ForcePartPressure(system, 1.0)
check_vtens_part(system, part)
def get_ff_polyethylene(**kwargs):
system = get_system_polyethylene4()
system = system.supercell(2)
fn_pars = pkg_resources.resource_filename(
__name__, '../../data/test/parameters_alkane.txt')
return ForceField.generate(system, fn_pars, **kwargs)
def test_topology_polyethylene4():
system = get_system_polyethylene4()
check_topology_slow(system)
def get_ff_polyethylene(**kwargs):
system = get_system_polyethylene4()
system = system.supercell(2)
fn_pars = context.get_fn('test/parameters_alkane.txt')
return ForceField.generate(system, fn_pars, **kwargs)
def get_ff_polyethylene(**kwargs):
system = get_system_polyethylene4()
system = system.supercell(2)
fn_pars = pkg_resources.resource_filename(__name__, '../../data/test/parameters_alkane.txt')
return ForceField.generate(system, fn_pars, **kwargs)
