def test_interrupt_simple(self):
sim = Simulation("SingleCPU")
sim.context.particle_types.add("A", 0.1)
# Define counter as list. This is a workaround because nosetest will complain otherwise.
counter = [0]
def increment(result):
counter[0] += 1
sim.register_observable_n_particles(1, ["A"], increment)
do_continue = lambda t: t < 5
sim.create_loop(.1).run_with_criterion(do_continue)
np.testing.assert_equal(counter[0], 6)
def test_write_trajectory(self):
traj_fname = os.path.join(self.dir, "traj.h5")
context = Context()
context.box_size = [5., 5., 5.]
context.particle_types.add("A", 0.0)
context.reactions.add_conversion("A->A", "A", "A", 1.)
simulation = Simulation("SingleCPU", context)
def callback(_):
simulation.add_particle("A", common.Vec(0, 0, 0))
simulation.register_observable_n_particles(1, ["A"], callback)
traj_handle = simulation.register_observable_trajectory(0)
with closing(io.File.create(traj_fname, io.FileFlag.OVERWRITE)) as f:
traj_handle.enable_write_to_file(f, u"", 3)
loop = simulation.create_loop(1.)
loop.write_config_to_file(f)
loop.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]))
with h5py.File(traj_fname, 'r') as f:
np.testing.assert_equal(
"A", f["readdy/config/particle_types"][0]["name"])
def test_write_trajectory(self):
traj_fname = os.path.join(self.dir, "traj.h5")
simulation = Simulation("SingleCPU")
simulation.context.box_size = [5., 5., 5.]
simulation.context.particle_types.add("A", 0.0)
simulation.context.reactions.add_conversion("A->A", "A", "A", 1.)
def callback(_):
simulation.add_particle("A", common.Vec(0, 0, 0))
simulation.register_observable_n_particles(1, ["A"], callback)
traj_handle = simulation.register_observable_trajectory(0)
with closing(io.File.create(traj_fname, io.FileFlag.OVERWRITE)) as f:
traj_handle.enable_write_to_file(f, u"", 3)
loop = simulation.create_loop(1.)
loop.write_config_to_file(f)
loop.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]))
with h5py.File(traj_fname) as f:
np.testing.assert_equal("A", f["readdy/config/particle_types"][0]["name"])
def test_sanity(self):
simulation = Simulation("SingleCPU")
loop = simulation.create_loop(1.)
loop.use_integrator("EulerBDIntegrator")
loop.evaluate_forces(False)
loop.use_reaction_scheduler("UncontrolledApproximation")
loop.evaluate_observables(False)
loop.run(10)
def test_reaction_counts_observable(self):
fname = os.path.join(self.dir,
"test_observables_particle_reaction_counts.h5")
context = Context()
context.box_size = [10., 10., 10.]
context.particle_types.add("A", .0)
context.particle_types.add("B", .0)
context.particle_types.add("C", .0)
context.reactions.add_conversion("mylabel", "A", "B", .00001)
context.reactions.add_conversion("A->B", "A", "B", 1e16)
context.reactions.add_fusion("B+C->A", "B", "C", "A", 1e16, 1.0, .5,
.5)
sim = Simulation("CPU", context)
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.create(fname)) as f:
handle.enable_write_to_file(f, u"reactions", int(3))
loop = sim.create_loop(1)
loop.use_reaction_scheduler("Gillespie")
loop.write_config_to_file(f)
loop.run(1)
import readdy.util.io_utils as io_utils
reactions = io_utils.get_reactions(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)
mylabel_id = get_item("mylabel", reactions.values())["id"]
atob_id = get_item("A->B", reactions.values())["id"]
fusion_id = get_item("B+C->A", reactions.values())["id"]
# counts of first time step, time is first index
np.testing.assert_equal(data["counts/" + str(mylabel_id)][0],
np.array([0]))
np.testing.assert_equal(data["counts/" + str(atob_id)][0],
np.array([0]))
np.testing.assert_equal(data["counts/" + str(fusion_id)][0],
np.array([0]))
# counts of second time step
np.testing.assert_equal(data["counts/" + str(mylabel_id)][1],
np.array([0]))
np.testing.assert_equal(data["counts/" + str(atob_id)][1],
np.array([1]))
np.testing.assert_equal(data["counts/" + str(fusion_id)][1],
np.array([1]))
def test_particles_observable(self):
fname = os.path.join(self.dir, "test_observables_particles.h5")
context = Context()
context.box_size = [13., 13., 13.]
context.particle_types.add("A", .1)
context.particle_types.add("B", .1)
sim = Simulation("SingleCPU", context)
sim.add_particle("A", common.Vec(0, 0, 0))
sim.add_particle("B", 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_particles(1)
n_timesteps = 19
with closing(io.File.create(fname)) as f:
handle.enable_write_to_file(f, u"particles", int(3))
loop = sim.create_loop(0)
loop.write_config_to_file(f)
loop.run(n_timesteps)
handle.flush()
from readdy.util.io_utils import get_particle_types
particle_types = get_particle_types(fname)
with h5py.File(fname, "r") as f2:
types = f2["readdy/observables/particles/types"][:]
ids = f2["readdy/observables/particles/ids"][:]
positions = f2["readdy/observables/particles/positions"][:]
for t in range(n_timesteps):
np.testing.assert_equal(len(types[t]), t + 3)
np.testing.assert_equal(len(ids[t]), t + 3)
np.testing.assert_equal(len(positions[t]), t + 3)
np.testing.assert_equal(types[t][0],
particle_types["A"]["type_id"])
np.testing.assert_equal(positions[t][0][0], 0)
np.testing.assert_equal(positions[t][0][1], 0)
np.testing.assert_equal(positions[t][0][2], 0)
np.testing.assert_equal(positions[t][1][0], 0)
np.testing.assert_equal(positions[t][1][1], 0)
np.testing.assert_equal(positions[t][1][2], 0)
np.testing.assert_equal(types[t][1],
particle_types["B"]["type_id"])
for others in range(2, len(types[t])):
np.testing.assert_equal(types[t][others],
particle_types["A"]["type_id"])
np.testing.assert_equal(positions[t][others][0], 1.5)
np.testing.assert_equal(positions[t][others][1], 2.5)
np.testing.assert_equal(positions[t][others][2], 3.5)
def test_reaction_counts_observable(self):
fname = os.path.join(self.dir, "test_observables_particle_reaction_counts.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", 1e16)
sim.context.reactions.add_fusion("B+C->A", "B", "C", "A", 1e16, 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.create(fname)) as f:
handle.enable_write_to_file(f, u"reactions", int(3))
loop = sim.create_loop(1)
loop.use_reaction_scheduler("Gillespie")
loop.write_config_to_file(f)
loop.run(1)
import readdy.util.io_utils as io_utils
reactions = io_utils.get_reactions(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)
mylabel_id = get_item("mylabel", reactions.values())["id"]
atob_id = get_item("A->B", reactions.values())["id"]
fusion_id = get_item("B+C->A", reactions.values())["id"]
# counts of first time step, time is first index
np.testing.assert_equal(data["counts/"+str(mylabel_id)][0], np.array([0]))
np.testing.assert_equal(data["counts/"+str(atob_id)][0], np.array([0]))
np.testing.assert_equal(data["counts/"+str(fusion_id)][0], np.array([0]))
# counts of second time step
np.testing.assert_equal(data["counts/"+str(mylabel_id)][1], np.array([0]))
np.testing.assert_equal(data["counts/"+str(atob_id)][1], np.array([1]))
np.testing.assert_equal(data["counts/"+str(fusion_id)][1], np.array([1]))
def test_particles_observable(self):
fname = os.path.join(self.dir, "test_observables_particles.h5")
sim = Simulation("SingleCPU")
sim.context.box_size = [13.,13.,13.]
sim.context.particle_types.add("A", .1)
sim.context.particle_types.add("B", .1)
sim.add_particle("A", common.Vec(0, 0, 0))
sim.add_particle("B", 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_particles(1)
n_timesteps = 19
with closing(io.File.create(fname)) as f:
handle.enable_write_to_file(f, u"particles", int(3))
loop = sim.create_loop(0)
loop.write_config_to_file(f)
loop.run(n_timesteps)
handle.flush()
from readdy.util.io_utils import get_particle_types
particle_types = get_particle_types(fname)
with h5py.File(fname, "r") as f2:
types = f2["readdy/observables/particles/types"][:]
ids = f2["readdy/observables/particles/ids"][:]
positions = f2["readdy/observables/particles/positions"][:]
for t in range(n_timesteps):
np.testing.assert_equal(len(types[t]), t + 3)
np.testing.assert_equal(len(ids[t]), t + 3)
np.testing.assert_equal(len(positions[t]), t + 3)
np.testing.assert_equal(types[t][0], particle_types["A"]["type_id"])
np.testing.assert_equal(positions[t][0][0], 0)
np.testing.assert_equal(positions[t][0][1], 0)
np.testing.assert_equal(positions[t][0][2], 0)
np.testing.assert_equal(positions[t][1][0], 0)
np.testing.assert_equal(positions[t][1][1], 0)
np.testing.assert_equal(positions[t][1][2], 0)
np.testing.assert_equal(types[t][1], particle_types["B"]["type_id"])
for others in range(2, len(types[t])):
np.testing.assert_equal(types[t][others], particle_types["A"]["type_id"])
np.testing.assert_equal(positions[t][others][0], 1.5)
np.testing.assert_equal(positions[t][others][1], 2.5)
np.testing.assert_equal(positions[t][others][2], 3.5)
def test_interrupt_maxparticles(self):
sim = Simulation("SingleCPU")
sim.context.particle_types.add("A", 0.1)
sim.add_particle("A", Vec(0, 0, 0))
sim.context.reactions.add_fission("bla", "A", "A", "A", 1000., 0., 0.5,
0.5)
counter = [0]
shall_stop = [False]
def increment(result):
counter[0] += 1
if result[0] >= 8:
shall_stop[0] = True
sim.register_observable_n_particles(1, ["A"], increment)
loop = sim.create_loop(1.)
do_continue = lambda t: not shall_stop[0]
loop.run_with_criterion(do_continue)
np.testing.assert_equal(counter[0], 4)
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"])