def test_seed(self):
tile_x = 1
tile_y = 1
thickness = 1.2
seed1 = 12345
seed2 = 54321
interface1 = mb.SilicaInterface(bulk_silica=AmorphousSilica(),
tile_x=tile_x,
tile_y=tile_y,
thickness=thickness,
seed=seed1)
atom_names1 = np.array([atom.name for atom in interface1.particles()])
interface2 = mb.SilicaInterface(bulk_silica=AmorphousSilica(),
tile_x=tile_x,
tile_y=tile_y,
thickness=thickness,
seed=seed1)
atom_names2 = np.array([atom.name for atom in interface2.particles()])
interface3 = mb.SilicaInterface(bulk_silica=AmorphousSilica(),
tile_x=tile_x,
tile_y=tile_y,
thickness=thickness,
seed=seed2)
atom_names3 = np.array([atom.name for atom in interface3.particles()])
assert np.array_equal(atom_names1, atom_names2)
assert not np.array_equal(atom_names1, atom_names3)
assert np.array_equal(interface1.xyz, interface2.xyz)
assert not np.array_equal(interface1.xyz, interface3.xyz)
def test_silica_interface(self):
tile_x = 1
tile_y = 1
thickness = 0.6
interface = mb.SilicaInterface(bulk_silica=AmorphousSilica(),
tile_x=tile_x,
tile_y=tile_y,
thickness=thickness)
thickness_tolerance = 0.05
z = [
atom.pos[2] for atom in interface.particles() if atom.name == 'Si'
]
assert abs(max(z) - min(z) - thickness) < thickness_tolerance
density_tolerance = 0.1
area = interface.periodicity[0] * interface.periodicity[1]
oh_count = len(list(interface.particles_by_name('OS')))
assert abs((oh_count / area) - 5.0) < density_tolerance
"""Label surface sites and add ports above them. """
for atom in self.particles():
if len(self.bond_graph.neighbors(atom)) == 1:
if atom.name == 'O' and atom.pos[2] > thickness:
atom.name = 'OS'
port = mb.Port(anchor=atom)
port.spin(np.pi/2, [1, 0, 0])
port.translate(np.array([0.0, 0.0, 0.1]))
self.add(port, "port_{}".format(len(self.referenced_ports())))
def _adjust_stoichiometry(self):
"""Remove O's from underside of surface to yield a 2:1 Si:O ratio. """
num_O = len(list(self.particles_by_name('O')))
num_Si = len(list(self.particles_by_name('Si')))
n_deletions = num_O - 2*num_Si
bottom_Os = [atom for atom in self.particles()
if atom.name == 'O' and
atom.pos[2] < self._O_buffer and
len(self.bond_graph.neighbors(atom)) == 1]
for _ in range(n_deletions):
O1 = random.choice(bottom_Os)
bottom_Os.remove(O1)
self.remove(O1)
if __name__ == "__main__":
from mbuild.lib.bulk_materials import AmorphousSilica
silica_interface = mb.SilicaInterface(bulk_silica=AmorphousSilica(), thickness=1.2)
silica_interface.save('silica_interface.mol2', show_ports=True)