def test_histogram_along_axis_observable(self):
fname = os.path.join(self.dir, "test_observables_hist_along_axis.h5")
context = Context()
context.kbt = 2
context.pbc = [True, True, True]
box_size = [10., 10., 10.]
context.box_size = box_size
context.particle_types.add("A", .2)
context.particle_types.add("B", .2)
context.potentials.add_harmonic_repulsion("A", "B", 10, 2.)
simulation = Simulation("SingleCPU", context)
simulation.add_particle("A", common.Vec(-2.5, 0, 0))
simulation.add_particle("B", common.Vec(0, 0, 0))
bin_borders = np.arange(0, 5, .01)
n_time_steps = 50
callback_hist = []
def hist_callback(hist):
callback_hist.append(hist)
handle = simulation.register_observable_histogram_along_axis(
2, bin_borders, 0, ["A", "B"], hist_callback)
with closing(io.File.create(fname)) as f:
handle.enable_write_to_file(f, u"hist_along_x_axis", int(3))
simulation.run(n_time_steps, 0.02)
handle.flush()
with h5py.File(fname, "r") as f2:
histogram = f2["readdy/observables/hist_along_x_axis/data"][:]
time_series = f2["readdy/observables/hist_along_x_axis/time"]
np.testing.assert_equal(time_series,
np.array(range(0, n_time_steps + 1))[::2])
for t in range(n_time_steps // 2):
np.testing.assert_equal(histogram[t],
np.array(callback_hist[t]))
def test_factory_programs(self):
kernel = pr.SingleCPUKernel()
kernel.get_kernel_context().particle_types().add("A", 1.0, 1.0)
factory = kernel.get_action_factory()
add_particles = factory.create_add_particles([pr.Particle(0, 0, 0, 0), pr.Particle(1, 1, 1, 0)])
integrator = factory.create_euler_integrator(1)
forces = factory.create_update_forces()
neighbor_list = factory.create_update_neighbor_list()
reactions = factory.create_reactions_uncontrolled_approximation(1)
add_particles.perform()
state_model = kernel.get_kernel_state_model()
positions = state_model.get_particle_positions()
np.testing.assert_equal(positions[0], cmn.Vec(0, 0, 0))
np.testing.assert_equal(positions[1], cmn.Vec(1, 1, 1))
it = kernel.get_kernel_state_model().get_particle_data().entries
assert next(it).pos == cmn.Vec(0, 0, 0)
assert next(it).pos == cmn.Vec(1, 1, 1)
with np.testing.assert_raises(StopIteration):
next(it)
def test_center_of_mass_observable(self):
common.set_logging_level("warn")
fname = os.path.join(self.dir, "test_observables_com.h5")
simulation = Simulation()
simulation.set_kernel("SingleCPU")
box_size = common.Vec(10, 10, 10)
simulation.kbt = 2
simulation.periodic_boundary = [True, True, True]
simulation.box_size = box_size
simulation.register_particle_type("A", .2, 1.)
simulation.register_particle_type("B", .2, 1.)
simulation.add_particle("A", common.Vec(-2.5, 0, 0))
simulation.add_particle("B", common.Vec(0, 0, 0))
n_time_steps = 50
callback_com = []
def com_callback(vec):
callback_com.append(vec)
handle = simulation.register_observable_center_of_mass(
1, ["A", "B"], com_callback)
with closing(
io.File(fname, io.FileAction.CREATE,
io.FileFlag.OVERWRITE)) as f:
handle.enable_write_to_file(f, u"com", 3)
simulation.run(n_time_steps, 0.02)
handle.flush()
with h5py.File(fname, "r") as f2:
com = f2["readdy/observables/com/data"][:]
for t in range(n_time_steps):
np.testing.assert_equal(com[t]["x"], callback_com[t][0])
np.testing.assert_equal(com[t]["y"], callback_com[t][1])
np.testing.assert_equal(com[t]["z"], callback_com[t][2])
def chain_decay(self, kernel):
sim = Simulation()
sim.set_kernel(kernel)
sim.box_size = common.Vec(10, 10, 10)
np.testing.assert_equal(sim.kernel_supports_topologies(), True)
typeid_b = sim.register_particle_type("B", 1.0, 1.0,
ParticleTypeFlavor.NORMAL)
sim.register_particle_type("Topology A", 1.0, 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(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())
# 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_unconnected_graph(self):
context = Context()
context.topologies.add_type("TA")
context.box_size = [10., 10., 10.]
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(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 test_radial_distribution_observable(self):
fname = os.path.join(self.dir, "test_observables_radial_distribution.h5")
simulation = Simulation("SingleCPU")
box_size = [10.,10.,10.]
simulation.context.kbt = 2
simulation.context.pbc = [True, True, True]
simulation.context.box_size = box_size
simulation.context.particle_types.add("A", .2)
simulation.context.particle_types.add("B", .2)
simulation.context.potentials.add_harmonic_repulsion("A", "B", 10, 2.)
simulation.add_particle("A", common.Vec(-2.5, 0, 0))
simulation.add_particle("B", common.Vec(0, 0, 0))
bin_borders = np.arange(0, 5, .01)
density = 1. / (box_size[0] * box_size[1] * box_size[2])
n_time_steps = 50
callback_centers = []
callback_rdf = []
def rdf_callback(pair):
callback_centers.append(pair[0])
callback_rdf.append(pair[1])
handle = simulation.register_observable_radial_distribution(1, bin_borders, ["A"], ["B"], density, rdf_callback)
with closing(io.File.create(fname)) as f:
handle.enable_write_to_file(f, u"radial_distribution", int(3))
simulation.run(n_time_steps, 0.02)
handle.flush()
with h5py.File(fname, "r") as f2:
bin_centers = f2["readdy/observables/radial_distribution/bin_centers"][:]
distribution = f2["readdy/observables/radial_distribution/distribution"][:]
for t in range(n_time_steps):
np.testing.assert_equal(bin_centers, np.array(callback_centers[t]))
np.testing.assert_equal(distribution[t], np.array(callback_rdf[t]))
def test_forces_observable(self):
fname = os.path.join(self.dir, "test_observables_particle_forces.h5")
sim = Simulation()
sim.set_kernel("CPU")
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_forces(1, [])
n_timesteps = 19
with closing(
io.File(fname, io.FileAction.CREATE,
io.FileFlag.OVERWRITE)) as f:
handle.enable_write_to_file(f, u"forces", int(3))
sim.run_scheme_readdy(True).configure(1).run(n_timesteps)
handle.flush()
with h5py.File(fname, "r") as f2:
data = f2["readdy/observables/forces/data"][:]
time_series = f2["readdy/observables/forces/time"]
np.testing.assert_equal(len(data), n_timesteps + 1)
np.testing.assert_equal(time_series,
np.array(range(0, n_timesteps + 1)))
for t, forces in enumerate(data):
# we begin with two particles
np.testing.assert_equal(len(forces), t + 2)
np.testing.assert_equal(forces[0]["x"], 0)
np.testing.assert_equal(forces[0]["y"], 0)
np.testing.assert_equal(forces[0]["z"], 0)
for i in range(1, len(forces)):
np.testing.assert_equal(forces[i]["x"], 0)
np.testing.assert_equal(forces[i]["y"], 0)
np.testing.assert_equal(forces[i]["z"], 0)
def test_kernel_context_shortest_difference(self):
self.ctx.box_size = [2, 2, 2]
self.ctx.pbc = [True, True, True]
self.ctx.configure()
diff = self.ctx.shortest_difference_fun
np.testing.assert_equal(diff(cmn.Vec(0, 0, 0), cmn.Vec(1, 0, 0)), cmn.Vec(1, 0, 0),
err_msg="both vectors were already inside the domain")
np.testing.assert_equal(diff(cmn.Vec(0, 0, 0), cmn.Vec(-1.5, 0, 0)), cmn.Vec(.5, 0, 0),
err_msg="The latter vector was outside the domain, thus had to get a "
"position update to (.5, 0, 0)")
def test_kernel_context_shortest_difference(self):
self.ctx.set_box_size(cmn.Vec(2, 2, 2))
self.ctx.periodic_boundary = [True, True, True]
diff = self.ctx.get_shortest_difference_fun()
np.testing.assert_equal(
diff(cmn.Vec(0, 0, 0), cmn.Vec(1, 0, 0)),
cmn.Vec(1, 0, 0),
err_msg="both vectors were already inside the domain")
np.testing.assert_equal(
diff(cmn.Vec(0, 0, 0), cmn.Vec(-1.5, 0, 0)),
cmn.Vec(.5, 0, 0),
err_msg=
"The latter vector was outside the domain, thus had to get a "
"position update to (.5, 0, 0)")
def test_custom_state_model(self):
class CustomStateModel(pr.Model):
def get_particle_positions(self):
return [cmn.Vec(-1, -1, -1)]
class CustomKernel(pr.SingleCPUKernel):
def __init__(self):
super(CustomKernel, self).__init__()
self._model = CustomStateModel(self.get_kernel_context(), self.get_topology_action_factory())
def get_kernel_state_model(self):
return self._model
kernel = CustomKernel()
pos = kernel.get_kernel_state_model().get_particle_positions()
assert len(pos) == 1
assert pos[0] == cmn.Vec(-1, -1, -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 chain_decay(self, kernel):
context = Context()
context.box_size = [10., 10., 10.]
context.topologies.add_type("TA")
context.particle_types.add("B", 1.0, ParticleTypeFlavor.NORMAL)
context.particle_types.add("Topology A", 1.0,
ParticleTypeFlavor.TOPOLOGY)
context.topologies.configure_bond_potential(
"Topology A", "Topology A",
BondedPotentialConfiguration(10, 10, "harmonic"))
context.topologies.add_structural_reaction("TA",
self._get_decay_reaction())
context.topologies.add_structural_reaction("TA",
self._get_split_reaction())
sim = Simulation(kernel, context)
np.testing.assert_equal(sim.kernel_supports_topologies(), True)
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)
# 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_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 test_reactions_observable(self):
common.set_logging_level("warn")
fname = os.path.join(self.dir,
"test_observables_particle_reactions.h5")
sim = Simulation()
sim.set_kernel("CPU")
sim.box_size = common.Vec(10, 10, 10)
sim.register_particle_type("A", .0, 5.0)
sim.register_particle_type("B", .0, 6.0)
sim.register_particle_type("C", .0, 6.0)
sim.register_reaction_conversion("mylabel", "A", "B", .00001)
sim.register_reaction_conversion("A->B", "A", "B", 1.)
sim.register_reaction_fusion("B+C->A", "B", "C", "A", 1.0, 1.0, .5, .5)
sim.add_particle("A", common.Vec(0, 0, 0))
sim.add_particle("B", common.Vec(1.0, 1.0, 1.0))
sim.add_particle("C", common.Vec(1.1, 1.0, 1.0))
n_timesteps = 1
handle = sim.register_observable_reactions(1)
with closing(
io.File(fname, io.FileAction.CREATE,
io.FileFlag.OVERWRITE)) as f:
handle.enable_write_to_file(f, u"reactions", int(3))
sim.run_scheme_readdy(True).write_config_to_file(
f).configure_and_run(n_timesteps, 1)
type_str_to_id = ioutils.get_particle_types(fname)
with h5py.File(fname, "r") as f2:
data = f2["readdy/observables/reactions"]
time_series = f2["readdy/observables/reactions/time"]
np.testing.assert_equal(time_series,
np.array(range(0, n_timesteps + 1)))
def get_item(name, collection):
return next(x for x in collection if x["name"] == name)
order_1_reactions = data["registered_reactions/order1_reactions"]
mylabel_reaction = get_item("mylabel", order_1_reactions)
np.testing.assert_equal(mylabel_reaction["rate"], .00001)
np.testing.assert_equal(mylabel_reaction["n_educts"], 1)
np.testing.assert_equal(mylabel_reaction["n_products"], 1)
np.testing.assert_equal(mylabel_reaction["educt_types"],
[type_str_to_id["A"], 0])
np.testing.assert_equal(mylabel_reaction["product_types"],
[type_str_to_id["B"], 0])
atob_reaction = get_item("A->B", order_1_reactions)
np.testing.assert_equal(atob_reaction["rate"], 1.)
np.testing.assert_equal(atob_reaction["n_educts"], 1)
np.testing.assert_equal(atob_reaction["n_products"], 1)
np.testing.assert_equal(mylabel_reaction["educt_types"],
[type_str_to_id["A"], 0])
np.testing.assert_equal(mylabel_reaction["product_types"],
[type_str_to_id["B"], 0])
order_2_reactions = data["registered_reactions/order2_reactions"]
fusion_reaction = get_item("B+C->A", order_2_reactions)
np.testing.assert_equal(fusion_reaction["rate"], 1.)
np.testing.assert_equal(fusion_reaction["educt_distance"], 1.)
np.testing.assert_equal(fusion_reaction["n_educts"], 2)
np.testing.assert_equal(fusion_reaction["n_products"], 1)
np.testing.assert_equal(fusion_reaction["educt_types"],
[type_str_to_id["B"], type_str_to_id["C"]])
np.testing.assert_equal(fusion_reaction["product_types"],
[type_str_to_id["A"], 0])
records = data["records"][:]
np.testing.assert_equal(len(records), 2)
# records of 1st time step
for record in records[1]:
np.testing.assert_equal(
record["reaction_type"] == 0
or record["reaction_type"] == 1, True)
if record["reaction_type"] == 0:
np.testing.assert_equal(record["position"],
np.array([.0, .0, .0]))
np.testing.assert_equal(record["reaction_index"], 1)
elif record["reaction_type"] == 1:
# fusion
np.testing.assert_equal(record["position"],
np.array([1.05, 1.0, 1.0]))
np.testing.assert_equal(record["reaction_index"], 0)
common.set_logging_level("warn")
def callback_all(hist):
callback_n_particles_all.append(hist)
simulation.add_particle("A", common.Vec(-1, -1, -1))
simulation.add_particle("B", common.Vec(-1, -1, -1))
def test_reactions_observable(self):
fname = os.path.join(self.dir, "test_observables_particle_reactions.h5")
sim = Simulation("CPU")
sim.context.box_size = [10.,10.,10.]
sim.context.particle_types.add("A", .0)
sim.context.particle_types.add("B", .0)
sim.context.particle_types.add("C", .0)
sim.context.reactions.add_conversion("mylabel", "A", "B", .00001)
sim.context.reactions.add_conversion("A->B", "A", "B", 1.)
sim.context.reactions.add_fusion("B+C->A", "B", "C", "A", 1.0, 1.0, .5, .5)
sim.add_particle("A", common.Vec(0, 0, 0))
sim.add_particle("B", common.Vec(1.0, 1.0, 1.0))
sim.add_particle("C", common.Vec(1.1, 1.0, 1.0))
n_timesteps = 1
handle = sim.register_observable_reactions(1)
with closing(io.File.create(fname)) as f:
handle.enable_write_to_file(f, u"reactions", int(3))
loop = sim.create_loop(1)
loop.write_config_to_file(f)
loop.run(n_timesteps)
type_str_to_id = {k: x["type_id"] for k, x in ioutils.get_particle_types(fname).items()}
with h5py.File(fname, "r") as f2:
data = f2["readdy/observables/reactions"]
time_series = f2["readdy/observables/reactions/time"]
np.testing.assert_equal(time_series, np.array(range(0, n_timesteps+1)))
def get_item(name, collection):
return next(x for x in collection if x["name"] == name)
import readdy.util.io_utils as io_utils
reactions = io_utils.get_reactions(fname)
mylabel_reaction = get_item("mylabel", reactions.values())
np.testing.assert_allclose(mylabel_reaction["rate"], .00001)
np.testing.assert_equal(mylabel_reaction["n_educts"], 1)
np.testing.assert_equal(mylabel_reaction["n_products"], 1)
np.testing.assert_equal(mylabel_reaction["educt_types"], [type_str_to_id["A"], 0])
np.testing.assert_equal(mylabel_reaction["product_types"], [type_str_to_id["B"], 0])
atob_reaction = get_item("A->B", reactions.values())
np.testing.assert_equal(atob_reaction["rate"], 1.)
np.testing.assert_equal(atob_reaction["n_educts"], 1)
np.testing.assert_equal(atob_reaction["n_products"], 1)
np.testing.assert_equal(mylabel_reaction["educt_types"], [type_str_to_id["A"], 0])
np.testing.assert_equal(mylabel_reaction["product_types"], [type_str_to_id["B"], 0])
fusion_reaction = get_item("B+C->A", reactions.values())
np.testing.assert_equal(fusion_reaction["rate"], 1.)
np.testing.assert_equal(fusion_reaction["educt_distance"], 1.)
np.testing.assert_equal(fusion_reaction["n_educts"], 2)
np.testing.assert_equal(fusion_reaction["n_products"], 1)
np.testing.assert_equal(fusion_reaction["educt_types"], [type_str_to_id["B"], type_str_to_id["C"]])
np.testing.assert_equal(fusion_reaction["product_types"], [type_str_to_id["A"], 0])
records = data["records"][:]
np.testing.assert_equal(len(records), 2)
# records of 1st time step
for record in records[1]:
np.testing.assert_equal(record["reaction_type"] == 0 or record["reaction_type"] == 1, True)
if record["reaction_type"] == 0:
np.testing.assert_equal(record["position"], np.array([.0, .0, .0]))
np.testing.assert_equal(record["reaction_id"], atob_reaction["id"])
elif record["reaction_type"] == 1:
# fusion
np.testing.assert_allclose(record["position"], np.array([1.05, 1.0, 1.0]))
np.testing.assert_equal(record["reaction_id"], fusion_reaction["id"])
def get_particle_positions(self):
return [cmn.Vec(-1, -1, -1)]
def callback_ab(value):
callback_n_particles_a_b.append(value)
simulation.add_particle("A", common.Vec(-1, -1, -1))
def test_kernel_context_dist_squared_fun(self):
self.ctx.box_size = [2., 2., 2.]
self.ctx.pbc = [True, True, True]
dist = self.ctx.dist_squared_fun
np.testing.assert_equal(dist(cmn.Vec(0, 0, 0), cmn.Vec(1, 0, 0)), 1.0)
np.testing.assert_equal(dist(cmn.Vec(-.5, 0, 0), cmn.Vec(-1.5, 0, 0)), 1.0)
def test_kernel_context_box_size(self):
self.ctx.set_box_size(cmn.Vec(5, 5, 5))
np.testing.assert_equal(self.ctx.get_box_size(), cmn.Vec(5, 5, 5))
def calculate_force(self, pos_vec):
return cmn.Vec(.1, .1, .1)
def test_reaction_counts_observable(self):
common.set_logging_level("warn")
fname = os.path.join(self.dir,
"test_observables_particle_reaction_counts.h5")
sim = Simulation()
sim.set_kernel("CPU")
sim.box_size = common.Vec(10, 10, 10)
sim.register_particle_type("A", .0, 5.0)
sim.register_particle_type("B", .0, 6.0)
sim.register_particle_type("C", .0, 6.0)
sim.register_reaction_conversion("mylabel", "A", "B", .00001)
sim.register_reaction_conversion("A->B", "A", "B", 1.)
sim.register_reaction_fusion("B+C->A", "B", "C", "A", 1.0, 1.0, .5, .5)
sim.add_particle("A", common.Vec(0, 0, 0))
sim.add_particle("B", common.Vec(1.0, 1.0, 1.0))
sim.add_particle("C", common.Vec(1.1, 1.0, 1.0))
n_timesteps = 1
handle = sim.register_observable_reaction_counts(1)
with closing(
io.File(fname, io.FileAction.CREATE,
io.FileFlag.OVERWRITE)) as f:
handle.enable_write_to_file(f, u"reactions", int(3))
sim.run_scheme_readdy(True).write_config_to_file(
f).with_reaction_scheduler(
"GillespieParallel").configure_and_run(n_timesteps, 1)
with h5py.File(fname, "r") as f2:
data = f2["readdy/observables/reactions"]
time_series = f2["readdy/observables/reactions/time"]
np.testing.assert_equal(time_series,
np.array(range(0, n_timesteps + 1)))
def get_item(name, collection):
return next(x for x in collection if x["name"] == name)
order_1_reactions = data["registered_reactions/order1_reactions"]
order_2_reactions = data["registered_reactions/order2_reactions"]
mylabel_reaction = get_item("mylabel", order_1_reactions)
reaction_idx_mylabel = mylabel_reaction["index"]
atob_reaction = get_item("A->B", order_1_reactions)
reaction_idx_atob = atob_reaction["index"]
# counts of first time step, time is first index
np.testing.assert_equal(
data["counts/order1/A[id=0]"][0, reaction_idx_mylabel],
np.array([0]))
np.testing.assert_equal(
data["counts/order1/A[id=0]"][0, reaction_idx_atob],
np.array([0]))
np.testing.assert_equal(
data["counts/order2/B[id=1] + C[id=2]"][0, 0], np.array([0]))
# counts of second time step
np.testing.assert_equal(
data["counts/order1/A[id=0]"][1, reaction_idx_mylabel],
np.array([0]))
np.testing.assert_equal(
data["counts/order1/A[id=0]"][1, reaction_idx_atob],
np.array([1]))
np.testing.assert_equal(
data["counts/order2/B[id=1] + C[id=2]"][1, 0], np.array([1]))
common.set_logging_level("warn")
def callback(_):
simulation.add_particle("A", common.Vec(0, 0, 0))
