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) 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.create(fname)) 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_histogram_along_axis_observable(self): fname = os.path.join(self.dir, "test_observables_hist_along_axis.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) 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_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_virial_observable_CPU(self): fname = os.path.join(self.dir, "test_observables_virial.h5") sim = Simulation("CPU") sim.context.box_size = [13., 13., 13.] sim.context.particle_types.add("A", .1) sim.context.potentials.add_harmonic_repulsion("A", "A", 10., .5) 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_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")
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) 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.create(fname)) 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)
class TestInternalSimulationModule(ReaDDyTestCase): def setUp(self): super().setUp() self.kernel_provider = KernelProvider.get() self.kernel_provider.load_from_dir(platform_utils.get_readdy_plugin_dir()) self.simulation = Simulation() def py_harmonic_repulsion_energy(self, x_ij): dist = x_ij * x_ij # if dist < sqrt(25): return energy with force constant 1 if dist < 25: return (np.sqrt(dist) - 5) ** 2 else: return 0 def py_harmonic_repulsion_force(self, x_ij): dist = x_ij * x_ij if dist < 25: dist = np.sqrt(dist) return (2 * (dist - 5) / dist) * x_ij else: return Vec(0, 0, 0) def test_properties(self): if not self.simulation.is_kernel_selected(): self.simulation.set_kernel('SingleCPU') np.testing.assert_equal(self.simulation.is_kernel_selected(), True) np.testing.assert_equal(self.simulation.get_selected_kernel_type(), "SingleCPU") self.simulation.kbt = 5.0 np.testing.assert_equal(self.simulation.kbt, 5.0) self.simulation.periodic_boundary = [True, False, True] np.testing.assert_equal(self.simulation.periodic_boundary, (True, False, True)) self.simulation.box_size = Vec(1, 3.6, 7) np.testing.assert_equal(self.simulation.box_size, Vec(1, 3.6, 7)) def py_position_observable_callback(self, positions): _vec_sum = Vec(0, 0, 0) for v in positions: _vec_sum += v mean = _vec_sum / float(len(positions)) print("mean=%s" % mean) def test_potentials(self): if not self.simulation.is_kernel_selected(): self.simulation.set_kernel("SingleCPU") ida = self.simulation.register_particle_type("ParticleTypeA", 1.0) idb = self.simulation.register_particle_type("ParticleTypeB", 3.0) self.simulation.register_particle_type("ParticleTypeA_internal", 1.0) self.simulation.register_particle_type("ParticleTypeB_internal", 3.0) pot = Pot2(ida, idb, self.py_harmonic_repulsion_energy, self.py_harmonic_repulsion_force) self.simulation.register_potential_order_2(pot) self.simulation.register_potential_harmonic_repulsion("ParticleTypeA_internal", "ParticleTypeB_internal", 1.0, 2.0) self.simulation.add_particle("ParticleTypeA", Vec(0, 0, 0)) self.simulation.add_particle("ParticleTypeB", Vec(0.4, 0.4, 0.4)) self.simulation.run(100, 1)
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_n_particles_observable(self): common.set_logging_level("warn") fname = os.path.join(self.dir, "test_observables_n_particles.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_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(fname, io.FileAction.CREATE, io.FileFlag.OVERWRITE)) 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_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_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_radial_distribution_observable(self): common.set_logging_level("warn") fname = os.path.join(self.dir, "test_observables_radial_distribution.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.register_potential_harmonic_repulsion("A", "B", 10) 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(fname, io.FileAction.CREATE, io.FileFlag.OVERWRITE)) 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_n_particles_observable(self): fname = os.path.join(self.dir, "test_observables_n_particles.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) simulation.register_particle_type("B", .2) 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") 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_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 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_particles_observable(self): fname = os.path.join(self.dir, "test_observables_particles.h5") sim = Simulation() sim.set_kernel("SingleCPU") sim.box_size = common.Vec(13, 13, 13) typeid_A = sim.register_particle_type("A", .1, .1) typeid_B = sim.register_particle_type("B", .1, .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(fname, io.FileAction.CREATE, io.FileFlag.OVERWRITE)) as f: handle.enable_write_to_file(f, u"particles", int(3)) sim.run_scheme_readdy(True).configure(0).run(n_timesteps) handle.flush() 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], typeid_A) 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], typeid_B) for others in range(2, len(types[t])): np.testing.assert_equal(types[t][others], typeid_A) 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() sim.set_kernel("SingleCPU") sim.register_particle_type("A", 0.1) sim.add_particle("A", Vec(0, 0, 0)) sim.register_reaction_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) scheme = sim.run_scheme_readdy(True).configure(1.) do_continue = lambda t: not shall_stop[0] scheme.run_with_criterion(do_continue) np.testing.assert_equal(counter[0], 4)
def test_histogram_along_axis_observable(self): common.set_logging_level("warn") fname = os.path.join(self.dir, "test_observables_hist_along_axis.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.register_potential_harmonic_repulsion("A", "B", 10) 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(fname, io.FileAction.CREATE, io.FileFlag.OVERWRITE)) 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_particles_observable(self): fname = os.path.join(self.dir, "test_observables_particles.h5") sim = Simulation() sim.set_kernel("SingleCPU") sim.box_size = common.Vec(13, 13, 13) typeid_A = sim.register_particle_type("A", .1) typeid_B = sim.register_particle_type("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)) sim.run_scheme_readdy(True).configure(0).run(n_timesteps) handle.flush() 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], typeid_A) 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], typeid_B) for others in range(2, len(types[t])): np.testing.assert_equal(types[t][others], typeid_A) 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") 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) simulation.register_particle_type("B", .2) simulation.register_potential_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_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 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 run(self): ################################### # # Units: # - [t] = sec # ################################### tau = 1e-3 kernel_provider = KernelProvider.get() kernel_provider.load_from_dir(platform_utils.get_readdy_plugin_dir()) simulation = Simulation() simulation.set_kernel("CPU") simulation.kbt = 1.0 simulation.box_size = Vec(3, 3, 3) simulation.periodic_boundary = [True, True, True] D = 1.0 R = .01 simulation.register_particle_type("A", D, R) simulation.register_particle_type("2A", D, R) simulation.register_particle_type("3A", D, R) simulation.register_particle_type("B", D, R) simulation.register_particle_type("GA", D, R) simulation.register_particle_type("GB", D, R) reaction_radius = .2 k1 = 4 * 1e-5 k2 = 50 k3 = 10 k4 = 250 V = simulation.box_size * simulation.box_size N_GA = 100.0 N_GB = 1000.0 k_enzymatic = brentq(lambda x: erban_chapman(k1, 2, reaction_radius, x), 1e-10, 5000000000000) k_enzymatic = 10. # k_enzymatic for reaction_radius = .1 print("k_enzymatic=%s" % k_enzymatic) print("2 * k3 - k3 * k3 * tau = %s" % (2.0 * k3 - k3 * k3 * tau)) print("k3 * k3 * tau = %s" % (k3 * k3 * tau)) print("k_birthA = %s" % (k2 * V / N_GA)) print("k_birthB = %s" % (k4 * V / N_GB)) print("sqrt(R*R/D) = %s" % (np.sqrt(reaction_radius * reaction_radius / D))) simulation.register_reaction_conversion("2A -> A", "2A", "A", 2.0 * k3 - k3 * k3 * tau) simulation.register_reaction_decay("2A -> 0", "2A", k3 * k3 * tau) simulation.register_reaction_fusion("A + A -> 2A", "A", "A", "2A", 1.0 / tau, reaction_radius, .5, .5) simulation.register_reaction_enzymatic("2A + B -> 2A + A", "2A", "B", "A", k_enzymatic, reaction_radius) simulation.register_reaction_fission("GA -> GA + A", "GA", "GA", "A", k2 * V / N_GA, reaction_radius, .5, .5) simulation.register_reaction_decay("A -> 0", "A", k3) simulation.register_reaction_fission("GB -> GB + B", "GB", "GB", "B", k4 * V / N_GB, reaction_radius, .5, .5) simulation.add_particle("A", Vec(0, 0, 0)) ga_x = np.random.uniform(-0.5 * simulation.box_size[0], 0.5 * simulation.box_size[0], int(N_GA)) ga_y = np.random.uniform(-0.5 * simulation.box_size[1], 0.5 * simulation.box_size[1], int(N_GA)) ga_z = np.random.uniform(-0.5 * simulation.box_size[2], 0.5 * simulation.box_size[2], int(N_GA)) gb_x = np.random.uniform(-0.5 * simulation.box_size[0], 0.5 * simulation.box_size[0], int(N_GB)) gb_y = np.random.uniform(-0.5 * simulation.box_size[1], 0.5 * simulation.box_size[1], int(N_GB)) gb_z = np.random.uniform(-0.5 * simulation.box_size[2], 0.5 * simulation.box_size[2], int(N_GB)) for i in range(int(N_GA)): simulation.add_particle("GA", Vec(ga_x[i], ga_y[i], ga_z[i])) for i in range(int(N_GB)): simulation.add_particle("GB", Vec(gb_x[i], gb_y[i], gb_z[i])) N_B = 30000 boxsize = np.array([simulation.box_size[0], simulation.box_size[1], simulation.box_size[2]]) for i in range(N_B): pos = np.random.random(3) * boxsize - 0.5 * boxsize simulation.add_particle("B", Vec(pos[0], pos[1], pos[2])) def callback(result): n_a, n_b = result[0] + 2 * result[1] + 3 * result[2], result[3] self._data[self._t, 0] = n_a self._data[self._t, 1] = n_b print("(%s,%s,a=%s,a2=%s,a3=%s)"%(n_a, n_b,result[0], result[1], result[2])) self.lines.set_xdata(self._data[:self._t, 0]) self.lines.set_ydata(self._data[:self._t, 1]) self.ax.relim() self.ax.autoscale_view() #We need to draw *and* flush self.fig.canvas.draw() self.fig.canvas.flush_events() plt.pause(.1) self._t += 1 simulation.register_observable_n_particles_types(1, ["A", "2A", "3A", "B"], callback) print("start run") simulation.run(self._timesteps, tau)
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 execute(self): ################################### # # Units: # - [x] = µm # - [t] = s # - [E] = kJ/mol # ################################### kernel_provider = KernelProvider.get() kernel_provider.load_from_dir(platform_utils.get_readdy_plugin_dir()) simulation = Simulation() simulation.set_kernel("CPU") ################################### # # set up simulation box # ################################### box_size = Vec(2, 7, 12) simulation.box_size = box_size simulation.kbt = 2.437 # room temperature simulation.periodic_boundary = [False, False, False] ################################### # # register particle types # ################################### # particle size, see: http://bmccellbiol.biomedcentral.com/articles/10.1186/1471-2121-5-29 # "The size of the V-ATPase complex is about 15 nm (diameter) x 25 nm (length from lumen side to tip of head)" membrane_particle_size = .05 diffusion_factor = .5 simulation.register_particle_type("D", 2.5 * diffusion_factor, .01) # MinD-ADP (without phosphor) simulation.register_particle_type("D_P", 2.5 * diffusion_factor, .01) # MinD-ATP (with phosphor) simulation.register_particle_type("E", 2.5 * diffusion_factor, .01) # MinE simulation.register_particle_type("D_PB", .01 * diffusion_factor, .01) # MinD-ATP bound simulation.register_particle_type("DE", .01 * diffusion_factor, .01) # MinDE ################################### # # register reaction types # ################################### reaction_radius = 4*(0.01 + 0.01) # = sum of the particle radii * 5 (5 - magic number such that k_fusion makes sense, sort of) 5 * # k_fusion = brentq(lambda x: self.erban_chapman(.093, 2.5 + .01, reaction_radius, x), 1, 5000000) k_fusion = 1.0 print("k_fusion=%s" % k_fusion) simulation.register_reaction_conversion("Phosphorylation", "D", "D_P", .5) simulation.register_reaction_fusion("bound MinD+MinE->MinDE", "D_PB", "E", "DE", k_fusion, reaction_radius*3.5, .5, .5) simulation.register_reaction_fission("MinDE to MinD and MinE, detach", "DE", "D", "E", .25, reaction_radius, .5, .5) ################################### # # register potentials # ################################### membrane_size = Vec(.5, 5, 10) layer = Vec(.08, .08, .08) extent = membrane_size + 2 * layer origin = -.5 * membrane_size - layer simulation.register_potential_box("D", 10., origin, extent, False) # (force constant, origin, extent, considerParticleRadius) simulation.register_potential_box("D_P", 10., origin, extent, False) # (force constant, origin, extent, considerParticleRadius) simulation.register_potential_box("D_PB", 10., origin, extent, False) # (force constant, origin, extent, considerParticleRadius) simulation.register_potential_box("E", 10., origin, extent, False) # (force constant, origin, extent, considerParticleRadius) simulation.register_potential_box("DE", 10., origin, extent, False) # (force constant, origin, extent, considerParticleRadius) # simulation.register_potential_piecewise_weak_interaction("D_P", "D_PB", 3, .02, 2, .05) # (force constant, desired dist, depth, no interaction dist) ################################### # # membrane particles # ################################### using_membrane_particles = False if using_membrane_particles: simulation.register_particle_type("M", 0, membrane_particle_size) # membrane particle simulation.register_reaction_enzymatic("Attach to membrane", "M", "D_P", "D_PB", .5, .01 + membrane_particle_size) # .01 + .025 # todo: rate? dx = np.linspace(origin[0] + layer[0], -1 * origin[0] - layer[0], int(float(membrane_size[0]) / membrane_particle_size), endpoint=True) dy = np.linspace(origin[1] + layer[1], -1 * origin[1] - layer[1], int(float(membrane_size[1]) / membrane_particle_size), endpoint=True) dz = np.linspace(origin[2] + layer[2], -1 * origin[2] - layer[2], int(float(membrane_size[2]) / membrane_particle_size), endpoint=True) for y in dy: for z in dz: simulation.add_particle("M", Vec(-1 * origin[0] - layer[0], y, z)) print("done adding membrane particles") else: simulation.register_reaction_conversion("Phosphorylation", "D_P", "D_PB", .5) simulation.register_reaction_enzymatic("Enzymatic DP+DPB->DPB + DPB", "D_PB", "D_P", "D_PB", .5, .02) using_uniform_distribution = True n_minE_particles = 3120 n_minD_particles = n_minE_particles * 4 mine_x = np.random.uniform(origin[0] + layer[0], -1 * origin[0] - layer[0], n_minE_particles) mine_y = np.random.uniform(origin[1] + layer[1], -1 * origin[1] - layer[1], n_minE_particles) if using_uniform_distribution: mine_z = np.random.uniform(origin[2] + layer[2], -1 * origin[2] - layer[2], n_minE_particles) else: mine_z = np.random.uniform(origin[2] + layer[2], .5 * (-1 * origin[2] - layer[2]), n_minE_particles) mind_x = np.random.uniform(origin[0] + layer[0], -1 * origin[0] - layer[0], n_minD_particles) mind_y = np.random.uniform(origin[1] + layer[1], -1 * origin[1] - layer[1], n_minD_particles) if using_uniform_distribution: mind_z = np.random.uniform(origin[2] + layer[2], -1 * origin[2] - layer[2], n_minD_particles) else: mind_z = np.random.uniform(.5 * (-1 * origin[2] - layer[2]), -1 * origin[2] - layer[2], n_minD_particles) for i in range(n_minE_particles): simulation.add_particle("E", Vec(mine_x[i], mine_y[i], mine_z[i])) for i in range(int(.5 * n_minD_particles)): simulation.add_particle("D", Vec(mind_x[i], mind_y[i], mind_z[i])) for i in range(int(.5 * n_minD_particles), n_minD_particles): simulation.add_particle("D_P", Vec(mind_x[i], mind_y[i], mind_z[i])) self.timestep = simulation.get_recommended_time_step(2) ################################### # # register observables # ################################### # simulation.register_observable_center_of_mass(1, self.com_callback_mind, ["D", "D_P", "D_PB"]) # simulation.register_observable_center_of_mass(1, self.com_callback_mine, ["E"]) # simulation.register_observable_center_of_mass(1, self.com_callback_minde, ["DE", "D_PB"]) print("histogram start") # simulation.register_observable_histogram_along_axis(100, self.histrogram_callback_minD, np.arange(-3, 3, .1), ["D", "D_P", "D_PB"], 2) # simulation.register_observable_histogram_along_axis(100, self.histrogram_callback_minE, np.arange(-3, 3, .1), ["D_PB", "DE"], 2) stride = int(.01/self.timestep) self.stride = stride print("using stride=%s" % stride) bins = np.linspace(-7, 7, 80) simulation.register_observable_histogram_along_axis(stride, bins, 2, ["D"], self.histogram_callback_minD) simulation.register_observable_histogram_along_axis(stride, bins, 2, ["D_P"], self.histogram_callback_minDP) simulation.register_observable_histogram_along_axis(stride, bins, 2, ["D_PB"], self.histogram_callback_minDPB) simulation.register_observable_histogram_along_axis(stride, bins, 2, ["E"], self.histogram_callback_minE) simulation.register_observable_histogram_along_axis(stride, bins, 2, ["DE"], self.histogram_callback_minDE) simulation.register_observable_histogram_along_axis(stride, bins, 2, ["D", "D_P", "D_PB", "DE"], self.histogram_callback_M) simulation.register_observable_n_particles(stride, ["D", "D_P", "D_PB", "E", "DE"], self.n_particles_callback) print("histogram end") self.n_timesteps = int(1200./self.timestep) print("starting simulation for effectively %s sec" % (self.timestep * self.n_timesteps)) simulation.run_scheme_readdy(True).with_reaction_scheduler("GillespieParallel").configure(self.timestep).run(self.n_timesteps) if self._result_fname is not None: with open(self._result_fname, 'w') as f: np.save(f, np.array(self._hist_data))
n_calls += 1 if n_calls % 10000 == 0: print("%s" % (10. * float(n_calls) / float(T))) if __name__ == '__main__': KernelProvider.get().load_from_dir(platform_utils.get_readdy_plugin_dir()) simulation = Simulation() simulation.set_kernel("CPU") box_size = 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.register_potential_harmonic_repulsion("A", "B", 10) simulation.add_particle("A", Vec(-2.5, 0, 0)) simulation.add_particle("B", Vec(0, 0, 0)) simulation.register_observable_radial_distribution( 10, np.arange(0, 5, .01), ["A"], ["B"], 1. / (box_size[0] * box_size[1] * box_size[2]), rdf_callback) simulation.run(T, 0.02) print("n_calls=%s" % n_calls) fig = plt.figure() ax = fig.add_subplot(111) ax.plot(centers, rdf / n_calls) plt.show()
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)
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 execute(self): ################################### # # Units: # - [x] = µm # - [t] = s # - [E] = kJ/mol # ################################### kernel_provider = KernelProvider.get() kernel_provider.load_from_dir(platform_utils.get_readdy_plugin_dir()) simulation = Simulation() simulation.set_kernel("CPU") ################################### # # set up simulation box # ################################### box_size = Vec(2, 7, 12) simulation.box_size = box_size simulation.kbt = 2.437 # room temperature simulation.periodic_boundary = [False, False, False] ################################### # # register particle types # ################################### # particle size, see: http://bmccellbiol.biomedcentral.com/articles/10.1186/1471-2121-5-29 # "The size of the V-ATPase complex is about 15 nm (diameter) x 25 nm (length from lumen side to tip of head)" membrane_particle_size = .05 diffusion_factor = .5 simulation.register_particle_type("D", 2.5 * diffusion_factor, .01) # MinD-ADP (without phosphor) simulation.register_particle_type("D_P", 2.5 * diffusion_factor, .01) # MinD-ATP (with phosphor) simulation.register_particle_type("E", 2.5 * diffusion_factor, .01) # MinE simulation.register_particle_type("D_PB", .01 * diffusion_factor, .01) # MinD-ATP bound simulation.register_particle_type("DE", .01 * diffusion_factor, .01) # MinDE ################################### # # register reaction types # ################################### reaction_radius = 4 * ( 0.01 + 0.01 ) # = sum of the particle radii * 5 (5 - magic number such that k_fusion makes sense, sort of) 5 * # k_fusion = brentq(lambda x: self.erban_chapman(.093, 2.5 + .01, reaction_radius, x), 1, 5000000) k_fusion = 1.0 print("k_fusion=%s" % k_fusion) simulation.register_reaction_conversion("Phosphorylation", "D", "D_P", .5) simulation.register_reaction_fusion("bound MinD+MinE->MinDE", "D_PB", "E", "DE", k_fusion, reaction_radius * 3.5, .5, .5) simulation.register_reaction_fission("MinDE to MinD and MinE, detach", "DE", "D", "E", .25, reaction_radius, .5, .5) ################################### # # register potentials # ################################### membrane_size = Vec(.5, 5, 10) layer = Vec(.08, .08, .08) extent = membrane_size + 2 * layer origin = -.5 * membrane_size - layer simulation.register_potential_box( "D", 10., origin, extent, False) # (force constant, origin, extent, considerParticleRadius) simulation.register_potential_box( "D_P", 10., origin, extent, False) # (force constant, origin, extent, considerParticleRadius) simulation.register_potential_box( "D_PB", 10., origin, extent, False) # (force constant, origin, extent, considerParticleRadius) simulation.register_potential_box( "E", 10., origin, extent, False) # (force constant, origin, extent, considerParticleRadius) simulation.register_potential_box( "DE", 10., origin, extent, False) # (force constant, origin, extent, considerParticleRadius) # simulation.register_potential_piecewise_weak_interaction("D_P", "D_PB", 3, .02, 2, .05) # (force constant, desired dist, depth, no interaction dist) ################################### # # membrane particles # ################################### using_membrane_particles = False if using_membrane_particles: simulation.register_particle_type( "M", 0, membrane_particle_size) # membrane particle simulation.register_reaction_enzymatic( "Attach to membrane", "M", "D_P", "D_PB", .5, .01 + membrane_particle_size) # .01 + .025 # todo: rate? dx = np.linspace( origin[0] + layer[0], -1 * origin[0] - layer[0], int(float(membrane_size[0]) / membrane_particle_size), endpoint=True) dy = np.linspace( origin[1] + layer[1], -1 * origin[1] - layer[1], int(float(membrane_size[1]) / membrane_particle_size), endpoint=True) dz = np.linspace( origin[2] + layer[2], -1 * origin[2] - layer[2], int(float(membrane_size[2]) / membrane_particle_size), endpoint=True) for y in dy: for z in dz: simulation.add_particle( "M", Vec(-1 * origin[0] - layer[0], y, z)) print("done adding membrane particles") else: simulation.register_reaction_conversion("Phosphorylation", "D_P", "D_PB", .5) simulation.register_reaction_enzymatic( "Enzymatic DP+DPB->DPB + DPB", "D_PB", "D_P", "D_PB", .5, .02) using_uniform_distribution = True n_minE_particles = 3120 n_minD_particles = n_minE_particles * 4 mine_x = np.random.uniform(origin[0] + layer[0], -1 * origin[0] - layer[0], n_minE_particles) mine_y = np.random.uniform(origin[1] + layer[1], -1 * origin[1] - layer[1], n_minE_particles) if using_uniform_distribution: mine_z = np.random.uniform(origin[2] + layer[2], -1 * origin[2] - layer[2], n_minE_particles) else: mine_z = np.random.uniform(origin[2] + layer[2], .5 * (-1 * origin[2] - layer[2]), n_minE_particles) mind_x = np.random.uniform(origin[0] + layer[0], -1 * origin[0] - layer[0], n_minD_particles) mind_y = np.random.uniform(origin[1] + layer[1], -1 * origin[1] - layer[1], n_minD_particles) if using_uniform_distribution: mind_z = np.random.uniform(origin[2] + layer[2], -1 * origin[2] - layer[2], n_minD_particles) else: mind_z = np.random.uniform(.5 * (-1 * origin[2] - layer[2]), -1 * origin[2] - layer[2], n_minD_particles) for i in range(n_minE_particles): simulation.add_particle("E", Vec(mine_x[i], mine_y[i], mine_z[i])) for i in range(int(.5 * n_minD_particles)): simulation.add_particle("D", Vec(mind_x[i], mind_y[i], mind_z[i])) for i in range(int(.5 * n_minD_particles), n_minD_particles): simulation.add_particle("D_P", Vec(mind_x[i], mind_y[i], mind_z[i])) self.timestep = simulation.get_recommended_time_step(2) ################################### # # register observables # ################################### # simulation.register_observable_center_of_mass(1, self.com_callback_mind, ["D", "D_P", "D_PB"]) # simulation.register_observable_center_of_mass(1, self.com_callback_mine, ["E"]) # simulation.register_observable_center_of_mass(1, self.com_callback_minde, ["DE", "D_PB"]) print("histogram start") # simulation.register_observable_histogram_along_axis(100, self.histrogram_callback_minD, np.arange(-3, 3, .1), ["D", "D_P", "D_PB"], 2) # simulation.register_observable_histogram_along_axis(100, self.histrogram_callback_minE, np.arange(-3, 3, .1), ["D_PB", "DE"], 2) stride = int(.01 / self.timestep) self.stride = stride print("using stride=%s" % stride) bins = np.linspace(-7, 7, 80) simulation.register_observable_histogram_along_axis( stride, bins, 2, ["D"], self.histogram_callback_minD) simulation.register_observable_histogram_along_axis( stride, bins, 2, ["D_P"], self.histogram_callback_minDP) simulation.register_observable_histogram_along_axis( stride, bins, 2, ["D_PB"], self.histogram_callback_minDPB) simulation.register_observable_histogram_along_axis( stride, bins, 2, ["E"], self.histogram_callback_minE) simulation.register_observable_histogram_along_axis( stride, bins, 2, ["DE"], self.histogram_callback_minDE) simulation.register_observable_histogram_along_axis( stride, bins, 2, ["D", "D_P", "D_PB", "DE"], self.histogram_callback_M) simulation.register_observable_n_particles( stride, ["D", "D_P", "D_PB", "E", "DE"], self.n_particles_callback) print("histogram end") self.n_timesteps = int(1200. / self.timestep) print("starting simulation for effectively %s sec" % (self.timestep * self.n_timesteps)) simulation.run_scheme_readdy(True).with_reaction_scheduler( "GillespieParallel").configure(self.timestep).run(self.n_timesteps) if self._result_fname is not None: with open(self._result_fname, 'w') as f: np.save(f, np.array(self._hist_data))
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)