def chain_decay(self, kernel):
sim = Simulation(kernel)
sim.context.box_size = [10., 10., 10.]
sim.context.topologies.add_type("TA")
np.testing.assert_equal(sim.kernel_supports_topologies(), True)
sim.context.particle_types.add("B", 1.0, ParticleTypeFlavor.NORMAL)
sim.context.particle_types.add("Topology A", 1.0, ParticleTypeFlavor.TOPOLOGY)
sim.context.topologies.configure_bond_potential("Topology A", "Topology A", BondedPotentialConfiguration(10, 10, "harmonic"))
n_elements = 50.
particles = [sim.create_topology_particle("Topology A", common.Vec(-5. + i * 10. / n_elements, 0, 0))
for i in range(int(n_elements))]
topology = sim.add_topology("TA", particles)
for i in range(int(n_elements - 1)):
topology.get_graph().add_edge(i, i + 1)
sim.context.topologies.add_structural_reaction("TA", self._get_decay_reaction())
sim.context.topologies.add_structural_reaction("TA", self._get_split_reaction())
# h = sim.register_observable_n_particles(1, [], lambda x: print("n particles=%s" % x))
np.testing.assert_equal(1, len(sim.current_topologies))
sim.run(500, 1.)
np.testing.assert_equal(0, len(sim.current_topologies))
def test_unbonded_edge(self):
context = Context()
context.box_size = [10., 10., 10.]
context.topologies.add_type("TA")
context.particle_types.add("T",
1.0,
flavor=ParticleTypeFlavor.TOPOLOGY)
context.particle_types.add("D",
1.0,
flavor=ParticleTypeFlavor.TOPOLOGY)
context.topologies.configure_bond_potential(
"T", "T", BondedPotentialConfiguration(10., 11., "harmonic"))
sim = Simulation("SingleCPU", context)
np.testing.assert_equal(sim.kernel_supports_topologies(), True)
particles = [
sim.create_topology_particle("T", common.Vec(0, 0, 0))
for _ in range(3)
]
particles.append(sim.create_topology_particle("D", common.Vec(0, 0,
0)))
top = sim.add_topology("TA", particles)
graph = top.get_graph()
graph.add_edge(0, 1)
graph.add_edge(1, 2)
graph.add_edge(2, 3)
with (np.testing.assert_raises(ValueError)):
top.configure()
def test_sanity(self):
context = Context()
context.box_size = [10., 10., 10.]
context.topologies.add_type("TA")
context.particle_types.add("T",
1.0,
flavor=ParticleTypeFlavor.TOPOLOGY)
context.topologies.configure_bond_potential(
"T", "T", BondedPotentialConfiguration(10., 11., "harmonic"))
sim = Simulation("SingleCPU", context)
np.testing.assert_equal(sim.kernel_supports_topologies(), True)
particles = [
sim.create_topology_particle("T", common.Vec(x, 0, 0))
for x in range(4)
]
top = sim.add_topology("TA", particles)
graph = top.graph
graph.add_edge(0, 1)
graph.add_edge(1, 2)
graph.add_edge(2, 3)
np.testing.assert_equal(len(graph.get_vertices()), 4)
for v in graph.vertices:
if v.particle_index == 0:
np.testing.assert_equal(top.position_of_vertex(v),
common.Vec(0, 0, 0))
np.testing.assert_equal(len(v.neighbors()), 1)
np.testing.assert_equal(
1 in [vv.get().particle_index for vv in v], True)
if v.particle_index == 1:
np.testing.assert_equal(top.position_of_vertex(v),
common.Vec(1, 0, 0))
np.testing.assert_equal(len(v.neighbors()), 2)
np.testing.assert_equal(
0 in [vv.get().particle_index for vv in v], True)
np.testing.assert_equal(
2 in [vv.get().particle_index for vv in v], True)
if v.particle_index == 2:
np.testing.assert_equal(top.position_of_vertex(v),
common.Vec(2, 0, 0))
np.testing.assert_equal(len(v.neighbors()), 2)
np.testing.assert_equal(
1 in [vv.get().particle_index for vv in v], True)
np.testing.assert_equal(
3 in [vv.get().particle_index for vv in v], True)
if v.particle_index == 3:
np.testing.assert_equal(top.position_of_vertex(v),
common.Vec(3, 0, 0))
np.testing.assert_equal(len(v.neighbors()), 1)
np.testing.assert_equal(
2 in [vv.get().particle_index for vv in v], True)
top.configure()
sim.run(0, 1)