def test_write_flat_trajectory(self):
common.set_logging_level("error")
traj_fname = os.path.join(self.dir, "flat_traj.h5")
simulation = Simulation()
simulation.set_kernel("SingleCPU")
simulation.box_size = common.Vec(5, 5, 5)
simulation.register_particle_type("A", 0.0, 0.0)
def callback(_):
simulation.add_particle("A", common.Vec(0, 0, 0))
simulation.register_observable_n_particles(1, ["A"], callback)
traj_handle = simulation.register_observable_flat_trajectory(1)
with closing(
io.File(traj_fname, io.FileAction.CREATE,
io.FileFlag.OVERWRITE)) as f:
traj_handle.enable_write_to_file(f, u"", int(3))
simulation.run_scheme_readdy(True).configure(1).run(20)
r = TrajectoryReader(traj_fname)
trajectory_items = r[:]
for idx, items in enumerate(trajectory_items):
np.testing.assert_equal(len(items), idx + 1)
for item in items:
np.testing.assert_equal(item.t, idx)
np.testing.assert_equal(item.position, np.array([.0, .0, .0]))
common.set_logging_level("debug")
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_write_flat_trajectory(self):
traj_fname = os.path.join(self.dir, "flat_traj.h5")
simulation = Simulation()
simulation.set_kernel("SingleCPU")
simulation.box_size = common.Vec(5,5,5)
simulation.register_particle_type("A", 0.0)
def callback(_):
simulation.add_particle("A", common.Vec(0, 0, 0))
simulation.register_observable_n_particles(1, ["A"], callback)
traj_handle = simulation.register_observable_flat_trajectory(1)
with closing(io.File.create(traj_fname, io.FileFlag.OVERWRITE)) as f:
traj_handle.enable_write_to_file(f, u"", int(3))
simulation.run_scheme_readdy(True).configure(1).run(20)
r = TrajectoryReader(traj_fname)
trajectory_items = r[:]
for idx, items in enumerate(trajectory_items):
np.testing.assert_equal(len(items), idx+1)
for item in items:
np.testing.assert_equal(item.t, idx)
np.testing.assert_equal(item.position, np.array([.0, .0, .0]))
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()))
