def test_nlist_graphene8_9A():
system = get_system_graphene8()
nlist = NeighborList(system)
rcut = 9*angstrom
nlist.request_rcut(rcut)
nlist.update()
nlist.check()
def test_nlist_graphene8_9A():
system = get_system_graphene8()
nlist = NeighborList(system)
rcut = 9 * angstrom
nlist.request_rcut(rcut)
nlist.update()
nlist.check()
def test_clean_momenta_2d():
sys = get_system_graphene8()
sys.set_standard_masses()
masses = sys.masses
vel = get_random_vel(300, False, masses)
com_mom = np.dot(masses, vel)
assert abs(com_mom).max() > 1e-10
clean_momenta(sys.pos, vel, masses, sys.cell)
com_mom = np.dot(masses, vel)
assert abs(com_mom).max() < 1e-10
def test_clean_momenta_2d():
sys = get_system_graphene8()
sys.set_standard_masses()
masses = sys.masses
vel = get_random_vel(300, False, masses)
com_mom = np.dot(masses, vel)
assert abs(com_mom).max() > 1e-10
clean_momenta(sys.pos, vel, masses, sys.cell)
com_mom = np.dot(masses, vel)
assert abs(com_mom).max() < 1e-10
def test_supercell_graphene_22():
system11 = get_system_graphene8()
system22 = system11.supercell(2, 2)
assert abs(system22.cell.volume - system11.cell.volume * 4) < 1e-10
assert abs(system22.cell.rvecs - system11.cell.rvecs * 2).max() < 1e-10
assert system22.natom == system11.natom * 4
assert system22.nbond == system11.nbond * 4
assert abs(system22.pos[8:16] - system11.pos -
system11.cell.rvecs[1]).max() < 1e-10
assert abs(system22.pos[-8:] - system11.pos -
system11.cell.rvecs.sum(axis=0)).max() < 1e-10
assert issubclass(system22.bonds.dtype.type, np.integer)
def test_cell_graphene8():
cell = get_system_graphene8().cell
assert abs(cell.volume - np.linalg.norm(np.cross(cell.rvecs[0], cell.rvecs[1]))) < 1e-10
assert abs(np.dot(cell.gvecs, cell.rvecs.transpose()) - np.identity(2)).max() < 1e-5
vec1 = np.array([10.0, 0.0, 105.0])*angstrom
cell.mic(vec1)
assert abs(vec1 - np.array([0.156, 0.0, 105])*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([1,2]))
assert abs(vec1 - np.array([10.002, 8.524, 105])*angstrom).max() < 1e-3
def test_cell_graphene8():
cell = get_system_graphene8().cell
assert abs(cell.volume - np.linalg.norm(np.cross(cell.rvecs[0], cell.rvecs[1]))) < 1e-10
assert abs(np.dot(cell.gvecs, cell.rvecs.transpose()) - np.identity(2)).max() < 1e-5
vec1 = np.array([10.0, 0.0, 105.0])*angstrom
cell.mic(vec1)
assert abs(vec1 - np.array([0.156, 0.0, 105])*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([1,2]))
assert abs(vec1 - np.array([10.002, 8.524, 105])*angstrom).max() < 1e-3
def test_nlist_inc_r2():
cell = get_system_graphene8().cell
rmax = np.array([2, 2])
r = np.array([-2, 1])
assert nlist_inc_r(cell, r, rmax)
assert (r == np.array([-1, 1])).all()
assert nlist_inc_r(cell, r, rmax)
assert (r == np.array([0, 1])).all()
assert nlist_inc_r(cell, r, rmax)
assert (r == np.array([1, 1])).all()
assert nlist_inc_r(cell, r, rmax)
assert (r == np.array([2, 1])).all()
assert nlist_inc_r(cell, r, rmax)
assert (r == np.array([-2, 2])).all()
assert nlist_inc_r(cell, r, rmax)
assert (r == np.array([-1, 2])).all()
r = np.array([2, 2])
assert not nlist_inc_r(cell, r, rmax)
assert (r == np.array([0, 0])).all()
def test_nlist_inc_r2():
cell = get_system_graphene8().cell
rmax = np.array([2, 2])
r = np.array([-2, 1])
assert nlist_inc_r(cell, r, rmax)
assert (r == np.array([-1, 1])).all()
assert nlist_inc_r(cell, r, rmax)
assert (r == np.array([0, 1])).all()
assert nlist_inc_r(cell, r, rmax)
assert (r == np.array([1, 1])).all()
assert nlist_inc_r(cell, r, rmax)
assert (r == np.array([2, 1])).all()
assert nlist_inc_r(cell, r, rmax)
assert (r == np.array([-2, 2])).all()
assert nlist_inc_r(cell, r, rmax)
assert (r == np.array([-1, 2])).all()
r = np.array([2, 2])
assert not nlist_inc_r(cell, r, rmax)
assert (r == np.array([0, 0])).all()
def test_topology_graphene8():
system = get_system_graphene8()
check_topology_slow(system)
def get_ff_graphene(**kwargs):
system = get_system_graphene8()
system = system.supercell(2, 2)
fn_pars = context.get_fn('test/parameters_polyene.txt')
return ForceField.generate(system, fn_pars, **kwargs)
def test_vtens_pext_2():
system = get_system_graphene8()
part = ForcePartPressure(system, 1.0)
check_vtens_part(system, part)
def test_topology_graphene8():
system = get_system_graphene8()
check_topology_slow(system)
def test_dlist_graphene8_bonds():
system = get_system_graphene8()
dlist = get_dlist_bonds(system)
check_dlist(system, dlist)
def test_dlist_graphene8_random():
system = get_system_graphene8()
dlist = get_dlist_random(system)
check_dlist(system, dlist)
def test_vtens_pext_2():
system = get_system_graphene8()
part = ForcePartPressure(system, 1.0)
check_vtens_part(system, part)
def get_ff_graphene(**kwargs):
system = get_system_graphene8()
system = system.supercell(2, 2)
fn_pars = pkg_resources.resource_filename(
__name__, '../../data/test/parameters_polyene.txt')
return ForceField.generate(system, fn_pars, **kwargs)
def get_ff_graphene(**kwargs):
system = get_system_graphene8()
system = system.supercell(2, 2)
fn_pars = context.get_fn('test/parameters_polyene.txt')
return ForceField.generate(system, fn_pars, **kwargs)
def test_iter_matches_peroxide_graphene8():
system0 = get_system_graphene8()
system1 = get_system_peroxide()
assert len(list(system0.iter_matches(system1))) == 0
def test_dlist_graphene8_random():
system = get_system_graphene8()
dlist = get_dlist_random(system)
check_dlist(system, dlist)
def test_dlist_graphene8_bonds():
system = get_system_graphene8()
dlist = get_dlist_bonds(system)
check_dlist(system, dlist)
def get_ff_graphene(**kwargs):
system = get_system_graphene8()
system = system.supercell(2, 2)
fn_pars = pkg_resources.resource_filename(__name__, '../../data/test/parameters_polyene.txt')
return ForceField.generate(system, fn_pars, **kwargs)
