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_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_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]))
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()