def test_unbonded_edge(self):
sim = Simulation()
sim.set_kernel("SingleCPU")
sim.box_size = common.Vec(10, 10, 10)
np.testing.assert_equal(sim.kernel_supports_topologies(), True)
sim.register_particle_type("T",
1.0,
.5,
flavor=ParticleTypeFlavor.TOPOLOGY)
sim.register_particle_type("D",
1.0,
.5,
flavor=ParticleTypeFlavor.TOPOLOGY)
sim.configure_topology_bond_potential("T", "T", 10., 11.)
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(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 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 chain_decay(self, kernel):
sim = Simulation()
sim.set_kernel(kernel)
sim.box_size = common.Vec(10, 10, 10)
sim.register_topology_type("TA")
np.testing.assert_equal(sim.kernel_supports_topologies(), True)
sim.register_particle_type("B", 1.0, ParticleTypeFlavor.NORMAL)
sim.register_particle_type("Topology A", 1.0, ParticleTypeFlavor.TOPOLOGY)
sim.configure_topology_bond_potential("Topology A", "Topology A", 10, 10)
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.register_structural_topology_reaction("TA", self._get_decay_reaction())
sim.register_structural_topology_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_scheme_readdy(True).evaluate_topology_reactions().configure_and_run(int(500), float(1.0))
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)
def test_sanity(self):
sim = Simulation()
sim.set_kernel("SingleCPU")
sim.box_size = common.Vec(10, 10, 10)
np.testing.assert_equal(sim.kernel_supports_topologies(), True)
sim.register_topology_type("TA")
sim.register_particle_type("T",
1.0,
flavor=ParticleTypeFlavor.TOPOLOGY)
sim.configure_topology_bond_potential("T", "T", 10., 11.)
particles = [
sim.create_topology_particle("T", common.Vec(x, 0, 0))
for x in range(4)
]
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)
np.testing.assert_equal(len(graph.get_vertices()), 4)
for v in graph.get_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_scheme_readdy(True).configure_and_run(0, 1)
def test_unconnected_graph(self):
sim = Simulation("SingleCPU")
sim.context.topologies.add_type("TA")
sim.context.box_size = [10., 10., 10.]
np.testing.assert_equal(sim.kernel_supports_topologies(), True)
sim.context.particle_types.add("T", 1.0, flavor=ParticleTypeFlavor.TOPOLOGY)
sim.context.topologies.configure_bond_potential("T", "T", BondedPotentialConfiguration(10, 11, "harmonic"))
particles = [sim.create_topology_particle("T", common.Vec(0, 0, 0)) for _ in range(4)]
top = sim.add_topology("TA", particles)
graph = top.get_graph()
graph.add_edge(0, 1)
graph.add_edge(1, 2)
with (np.testing.assert_raises(ValueError)):
top.configure()
def run(self, time_steps, out_file):
sim = Simulation()
sim.set_kernel(self.kernel)
sim.box_size = common.Vec(60, 20, 20)
sim.periodic_boundary = [True, True, True]
typeid_b = sim.register_particle_type("B", 1.0, 1.0,
ParticleTypeFlavor.NORMAL)
sim.register_particle_type("Topology A", .5, .5,
ParticleTypeFlavor.TOPOLOGY)
sim.register_potential_harmonic_repulsion("Topology A", "Topology A",
10)
sim.register_potential_harmonic_repulsion("Topology A", "B", 10)
sim.register_potential_harmonic_repulsion("B", "B", 10)
sim.configure_topology_bond_potential("Topology A", "Topology A", 10,
1.)
sim.configure_topology_angle_potential("Topology A", "Topology A",
"Topology A", 10, np.pi)
# sim.configure_topology_dihedral_potential("Topology A", "Topology A", "Topology A", "Topology A", 1, 1, -np.pi)
n_elements = 50.
particles = [
sim.create_topology_particle("Topology A",
common.Vec(-25. + i, 0, 0))
for i in range(int(n_elements))
]
topology = sim.add_topology(particles)
for i in range(int(n_elements - 1)):
topology.get_graph().add_edge(i, i + 1)
topology.add_reaction(self._get_decay_reaction(typeid_b))
topology.add_reaction(self._get_split_reaction())
traj_handle = sim.register_observable_flat_trajectory(1)
with closing(
io.File(out_file, io.FileAction.CREATE,
io.FileFlag.OVERWRITE)) as f:
traj_handle.enable_write_to_file(f, u"", 50)
sim.run_scheme_readdy(True)\
.evaluate_topology_reactions()\
.write_config_to_file(f)\
.configure_and_run(time_steps, self.time_step)
print("currently %s topologies" % len(sim.current_topologies()))
def test_unbonded_edge(self):
sim = Simulation()
sim.set_kernel("SingleCPU")
sim.box_size = common.Vec(10, 10, 10)
sim.register_topology_type("TA")
np.testing.assert_equal(sim.kernel_supports_topologies(), True)
sim.register_particle_type("T", 1.0, flavor=ParticleTypeFlavor.TOPOLOGY)
sim.register_particle_type("D", 1.0, flavor=ParticleTypeFlavor.TOPOLOGY)
sim.configure_topology_bond_potential("T", "T", 10., 11.)
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):
sim = Simulation()
sim.set_kernel("SingleCPU")
sim.box_size = common.Vec(10, 10, 10)
np.testing.assert_equal(sim.kernel_supports_topologies(), True)
sim.register_particle_type("T",
1.0,
.5,
flavor=ParticleTypeFlavor.TOPOLOGY)
sim.configure_topology_bond_potential("T", "T", 10., 11.)
particles = [
sim.create_topology_particle("T", common.Vec(0, 0, 0))
for _ in range(4)
]
labels = ["%s" % i for i in range(4)]
top = sim.add_topology(particles, labels)
graph = top.get_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.get_vertices():
if v.label == "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.label == "1":
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.label == "2":
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.label == "3":
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_scheme_readdy(True).configure_and_run(0, 1)
def chain_decay(self, kernel):
sim = Simulation()
sim.set_kernel(kernel)
sim.box_size = common.Vec(10, 10, 10)
sim.register_topology_type("TA")
np.testing.assert_equal(sim.kernel_supports_topologies(), True)
sim.register_particle_type("B", 1.0, ParticleTypeFlavor.NORMAL)
sim.register_particle_type("Topology A", 1.0,
ParticleTypeFlavor.TOPOLOGY)
sim.configure_topology_bond_potential("Topology A", "Topology A", 10,
10)
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.register_structural_topology_reaction("TA",
self._get_decay_reaction())
sim.register_structural_topology_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_scheme_readdy(
True).evaluate_topology_reactions().configure_and_run(
int(500), float(1.0))
np.testing.assert_equal(0, len(sim.current_topologies()))
def test_sanity(self):
sim = Simulation("SingleCPU")
sim.context.box_size = [10., 10., 10.]
np.testing.assert_equal(sim.kernel_supports_topologies(), True)
sim.context.topologies.add_type("TA")
sim.context.particle_types.add("T", 1.0, flavor=ParticleTypeFlavor.TOPOLOGY)
sim.context.topologies.configure_bond_potential("T", "T", BondedPotentialConfiguration(10., 11., "harmonic"))
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)
def test_sanity(self):
sim = Simulation()
sim.set_kernel("SingleCPU")
sim.box_size = common.Vec(10, 10, 10)
np.testing.assert_equal(sim.kernel_supports_topologies(), True)
sim.register_topology_type("TA")
sim.register_particle_type("T", 1.0, flavor=ParticleTypeFlavor.TOPOLOGY)
sim.configure_topology_bond_potential("T", "T", 10., 11.)
particles = [sim.create_topology_particle("T", common.Vec(x, 0, 0)) for x in range(4)]
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)
np.testing.assert_equal(len(graph.get_vertices()), 4)
for v in graph.get_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_scheme_readdy(True).configure_and_run(0, 1)
def run(self, time_steps, out_file):
sim = Simulation()
sim.set_kernel(self.kernel)
sim.box_size = common.Vec(60, 20, 20)
sim.periodic_boundary = [True, True, True]
typeid_b = sim.register_particle_type("B", 1.0, 1.0, ParticleTypeFlavor.NORMAL)
sim.register_particle_type("Topology A", .5, .5, ParticleTypeFlavor.TOPOLOGY)
sim.register_potential_harmonic_repulsion("Topology A", "Topology A", 10)
sim.register_potential_harmonic_repulsion("Topology A", "B", 10)
sim.register_potential_harmonic_repulsion("B", "B", 10)
sim.configure_topology_bond_potential("Topology A", "Topology A", 10, 1.)
sim.configure_topology_angle_potential("Topology A", "Topology A", "Topology A", 10, np.pi)
# sim.configure_topology_dihedral_potential("Topology A", "Topology A", "Topology A", "Topology A", 1, 1, -np.pi)
n_elements = 50.
particles = [sim.create_topology_particle("Topology A", common.Vec(-25. + i, 0, 0))
for i in range(int(n_elements))]
topology = sim.add_topology(particles)
for i in range(int(n_elements - 1)):
topology.get_graph().add_edge(i, i + 1)
topology.add_reaction(self._get_decay_reaction(typeid_b))
topology.add_reaction(self._get_split_reaction())
traj_handle = sim.register_observable_flat_trajectory(1)
with closing(io.File(out_file, io.FileAction.CREATE, io.FileFlag.OVERWRITE)) as f:
traj_handle.enable_write_to_file(f, u"", 50)
sim.run_scheme_readdy(True)\
.evaluate_topology_reactions()\
.write_config_to_file(f)\
.configure_and_run(time_steps, self.time_step)
print("currently %s topologies" % len(sim.current_topologies()))
