def test_particle_positions_observable(self):
fname = os.path.join(self.dir, "test_observables_particle_positions.h5")
sim = Simulation("SingleCPU")
sim.context.box_size = [13., 13., 13.]
sim.context.particle_types.add("A", .1)
sim.add_particle("A", common.Vec(0, 0, 0))
# every time step, add one particle
sim.register_observable_n_particles(1, ["A"], lambda n: sim.add_particle("A", common.Vec(1.5, 2.5, 3.5)))
handle = sim.register_observable_particle_positions(1, [])
n_timesteps = 19
with closing(io.File.create(fname)) as f:
handle.enable_write_to_file(f, u"particle_positions", int(3))
sim.run(n_timesteps, 0)
handle.flush()
with h5py.File(fname, "r") as f2:
data = f2["readdy/observables/particle_positions/data"][:]
np.testing.assert_equal(len(data), n_timesteps + 1)
for t, positions in enumerate(data):
# we begin with two particles
np.testing.assert_equal(len(positions), t + 2)
np.testing.assert_equal(positions[0]["x"], 0)
np.testing.assert_equal(positions[0]["y"], 0)
np.testing.assert_equal(positions[0]["z"], 0)
for i in range(1, len(positions)):
np.testing.assert_equal(positions[i]["x"], 1.5)
np.testing.assert_equal(positions[i]["y"], 2.5)
np.testing.assert_equal(positions[i]["z"], 3.5)
def test_particle_positions_observable(self):
fname = os.path.join(self.dir,
"test_observables_particle_positions.h5")
sim = Simulation()
sim.set_kernel("SingleCPU")
sim.box_size = common.Vec(13, 13, 13)
sim.register_particle_type("A", .1, .1)
sim.add_particle("A", common.Vec(0, 0, 0))
# every time step, add one particle
sim.register_observable_n_particles(
1, ["A"],
lambda n: sim.add_particle("A", common.Vec(1.5, 2.5, 3.5)))
handle = sim.register_observable_particle_positions(1, [])
n_timesteps = 19
with closing(
io.File(fname, io.FileAction.CREATE,
io.FileFlag.OVERWRITE)) as f:
handle.enable_write_to_file(f, u"particle_positions", int(3))
sim.run_scheme_readdy(True).configure(0).run(n_timesteps)
handle.flush()
with h5py.File(fname, "r") as f2:
data = f2["readdy/observables/particle_positions/data"][:]
np.testing.assert_equal(len(data), n_timesteps + 1)
for t, positions in enumerate(data):
# we begin with two particles
np.testing.assert_equal(len(positions), t + 2)
np.testing.assert_equal(positions[0]["x"], 0)
np.testing.assert_equal(positions[0]["y"], 0)
np.testing.assert_equal(positions[0]["z"], 0)
for i in range(1, len(positions)):
np.testing.assert_equal(positions[i]["x"], 1.5)
np.testing.assert_equal(positions[i]["y"], 2.5)
np.testing.assert_equal(positions[i]["z"], 3.5)
common.set_logging_level("warn")
class TwoParticlesMiniExample(object):
def __init__(self):
KernelProvider.get().load_from_dir(
platform_utils.get_readdy_plugin_dir())
self.simulation = Simulation()
self.simulation.set_kernel("CPU")
self.fig = plt.figure()
self.ax = self.fig.add_subplot(111, projection='3d')
plt.ioff()
self.fig.show()
self.prev_pos = {}
self.current_plot = None
self.T = 4000000
def ppos_callback(self, pos):
plt.cla()
self.ax.set_xlim([-1, 1])
self.ax.set_ylim([-1, 1])
self.ax.set_zlim([-1, 1])
r = [-.75, .75]
for s, e in combinations(np.array(list(product(r, r, r))), 2):
if np.sum(np.abs(s - e)) == r[1] - r[0]:
self.ax.plot3D(*zip(s, e), color="b")
pA = self.simulation.get_particle_positions("A")
pB = self.simulation.get_particle_positions("B")
if len(pA) == 1 and len(pB) == 1:
A = pA[0]
B = pB[0]
self.ax.scatter([A[0]], [A[1]], [A[2]], color="g", s=100)
self.ax.scatter([B[0]], [B[1]], [B[2]], color="r", s=100)
self.ax.plot3D([A[0], B[0]], [A[1], B[1]], [A[2], B[2]], color="r")
pC = self.simulation.get_particle_positions("C")
if len(pC) == 1:
C = pC[0]
self.ax.scatter([C[0]], [C[1]], [C[2]], color="b", s=100)
plt.pause(.001)
def start(self):
box_size = Vec(2.0, 2.0, 2.0)
depth = 2.
desired_dist = .25
force_constant = 4 * depth / (desired_dist * desired_dist)
no_interaction_dist = 1.5
self.simulation.kbt = 0.01
self.simulation.periodic_boundary = [False, False, False]
self.simulation.box_size = box_size
self.simulation.register_particle_type("A", .1, .1)
self.simulation.register_particle_type("B", .01, .1)
self.simulation.register_particle_type("C", .5, .1)
self.simulation.register_potential_piecewise_weak_interaction(
"A", "B", force_constant, desired_dist, depth, no_interaction_dist
) # (force constant, desired dist, depth, no interaction dist)
self.simulation.register_reaction_fusion("fusion", "A", "B", "C",
1000., .3, .5, .5)
self.simulation.register_reaction_fission("fission", "C", "A", "B",
1000., .25, .5, .5)
self.simulation.register_potential_box("A", 100.,
Vec(-.75, -.75, -.75),
Vec(1.5, 1.5, 1.5), False)
self.simulation.register_potential_box("B", 100.,
Vec(-.75, -.75, -.75),
Vec(1.5, 1.5, 1.5), False)
self.simulation.register_potential_box("C", 100.,
Vec(-.75, -.75, -.75),
Vec(1.5, 1.5, 1.5), False)
self.simulation.add_particle("A", Vec(-.0, -.0, -.0))
self.simulation.add_particle("B", Vec(0.1, 0.1, 0.1))
self.simulation.register_observable_particle_positions(
1, [], self.ppos_callback)
self.simulation.run(self.T, .0001)
class TwoParticlesMiniExample(object):
def __init__(self):
KernelProvider.get().load_from_dir(platform_utils.get_readdy_plugin_dir())
self.simulation = Simulation()
self.simulation.set_kernel("CPU")
self.fig = plt.figure()
self.ax = self.fig.add_subplot(111, projection='3d')
plt.ioff()
self.fig.show()
self.prev_pos = {}
self.current_plot = None
self.T = 4000000
def ppos_callback(self, pos):
plt.cla()
self.ax.set_xlim([-1, 1])
self.ax.set_ylim([-1, 1])
self.ax.set_zlim([-1, 1])
r = [-.75, .75]
for s, e in combinations(np.array(list(product(r, r, r))), 2):
if np.sum(np.abs(s - e)) == r[1] - r[0]:
self.ax.plot3D(*zip(s, e), color="b")
pA = self.simulation.get_particle_positions("A")
pB = self.simulation.get_particle_positions("B")
if len(pA) == 1 and len(pB) == 1:
A = pA[0]; B = pB[0]
self.ax.scatter([A[0]], [A[1]], [A[2]], color="g", s=100)
self.ax.scatter([B[0]], [B[1]], [B[2]], color="r", s=100)
self.ax.plot3D([A[0], B[0]], [A[1], B[1]], [A[2], B[2]], color="r")
pC = self.simulation.get_particle_positions("C")
if len(pC) == 1:
C = pC[0]
self.ax.scatter([C[0]], [C[1]], [C[2]], color="b", s=100)
plt.pause(.001)
def start(self):
box_size = Vec(2.0, 2.0, 2.0)
depth = 2.
desired_dist = .25
force_constant = 4 * depth / (desired_dist * desired_dist)
no_interaction_dist = 1.5
self.simulation.kbt = 0.01
self.simulation.periodic_boundary = [False, False, False]
self.simulation.box_size = box_size
self.simulation.register_particle_type("A", .1, .1)
self.simulation.register_particle_type("B", .01, .1)
self.simulation.register_particle_type("C", .5, .1)
self.simulation.register_potential_piecewise_weak_interaction("A", "B", force_constant, desired_dist, depth,
no_interaction_dist) # (force constant, desired dist, depth, no interaction dist)
self.simulation.register_reaction_fusion("fusion", "A", "B", "C", 1000., .3, .5, .5)
self.simulation.register_reaction_fission("fission", "C", "A", "B", 1000., .25, .5, .5)
self.simulation.register_potential_box("A", 100., Vec(-.75, -.75, -.75), Vec(1.5, 1.5, 1.5), False)
self.simulation.register_potential_box("B", 100., Vec(-.75, -.75, -.75), Vec(1.5, 1.5, 1.5), False)
self.simulation.register_potential_box("C", 100., Vec(-.75, -.75, -.75), Vec(1.5, 1.5, 1.5), False)
self.simulation.add_particle("A", Vec(-.0, -.0, -.0))
self.simulation.add_particle("B", Vec(0.1, 0.1, 0.1))
self.simulation.register_observable_particle_positions(1, [], self.ppos_callback)
self.simulation.run(self.T, .0001)
