def test_particle_positions_observable(self):
fname = os.path.join(self.dir,
"test_observables_particle_positions.h5")
context = Context()
context.box_size = [13., 13., 13.]
context.particle_types.add("A", .1)
sim = Simulation("SingleCPU", context)
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_virial_observable_SCPU(self):
fname = os.path.join(self.dir, "test_observables_virial_scpu.h5")
context = Context()
context.box_size = [13., 13., 13.]
context.particle_types.add("A", .1)
context.potentials.add_harmonic_repulsion("A", "A", 10., .5)
sim = Simulation("SingleCPU", context)
for _ in range(10000):
pos = common.Vec(*(13 * np.random.random(size=3) - .5 * 13))
sim.add_particle("A", pos)
virials = []
def virial_callback(virial):
virials.append(np.ndarray((3, 3), buffer=virial))
handle = sim.register_observable_virial(1, virial_callback)
with closing(io.File.create(fname)) as f:
handle.enable_write_to_file(f, u"virial", int(3))
sim.run(10, .1)
handle.flush()
with h5py.File(fname, "r") as f2:
h5virials = f2["readdy/observables/virial/data"]
for v, v2 in zip(virials, h5virials):
np.testing.assert_almost_equal(v, v2)
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_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_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_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_n_particles_observable(self):
fname = os.path.join(self.dir, "test_observables_n_particles.h5")
context = Context()
box_size = [10., 10., 10.]
context.kbt = 2
context.pbc = [True, True, True]
context.box_size = box_size
context.particle_types.add("A", .2)
context.particle_types.add("B", .2)
simulation = Simulation("SingleCPU", context)
simulation.add_particle("A", common.Vec(-2.5, 0, 0))
simulation.add_particle("B", common.Vec(0, 0, 0))
n_time_steps = 50
callback_n_particles_a_b = []
callback_n_particles_all = []
def callback_ab(value):
callback_n_particles_a_b.append(value)
simulation.add_particle("A", common.Vec(-1, -1, -1))
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))
handle_a_b_particles = simulation.register_observable_n_particles(
1, ["A", "B"], callback_ab)
handle_all = simulation.register_observable_n_particles(
1, [], callback_all)
with closing(io.File.create(fname)) as f:
handle_a_b_particles.enable_write_to_file(f, u"n_a_b_particles",
int(3))
handle_all.enable_write_to_file(f, u"n_particles", int(5))
simulation.run(n_time_steps, 0.02)
handle_all.flush()
handle_a_b_particles.flush()
with h5py.File(fname, "r") as f2:
n_a_b_particles = f2["readdy/observables/n_a_b_particles/data"][:]
n_particles = f2["readdy/observables/n_particles/data"][:]
time_series = f2["readdy/observables/n_a_b_particles/time"]
np.testing.assert_equal(time_series,
np.array(range(0, n_time_steps + 1)))
for t in range(n_time_steps):
np.testing.assert_equal(n_a_b_particles[t][0],
callback_n_particles_a_b[t][0])
np.testing.assert_equal(n_a_b_particles[t][1],
callback_n_particles_a_b[t][1])
np.testing.assert_equal(n_particles[t][0],
callback_n_particles_all[t][0])
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_radial_distribution_observable(self):
fname = os.path.join(self.dir,
"test_observables_radial_distribution.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)
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 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_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_write_trajectory_as_observable(self):
traj_fname = os.path.join(self.dir, "traj_as_obs.h5")
context = Context()
context.box_size = [5., 5., 5.]
context.particle_types.add("A", 0.0)
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(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(20, 1)
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):
fname = os.path.join(self.dir,
"test_observables_particle_reactions.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", 1.)
context.reactions.add_fusion("B+C->A", "B", "C", "A", 1.0, 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_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"])