def test_potential_order_2(self):
self.ctx.box_size = [2, 2, 2]
self.ctx.pbc = [True, True, True]
self.model.get_particle_data().clear()
class MyPot2(pr.PotentialOrder2):
def __init__(self, typea, typeb):
super(MyPot2, self).__init__(typea, typeb)
def calculate_energy(self, x_ij):
return np.sqrt(x_ij * x_ij)
def calculate_force(self, x_ij):
return .5 * x_ij
def configure_for_types(self, type1, type2):
pass
def get_cutoff_radius(self):
return 5.0
def get_maximal_force(self, kbt):
return kbt
self.ctx.particle_types.add("A", 1.0, 0)
self.ctx.particle_types.add("B", 1.0, 0)
pot = MyPot2(self.ctx.particle_types.id_of("A"), self.ctx.particle_types.id_of("B"))
self.ctx.potentials.add_external_order2(pot)
particles = [pr.Particle(0, 0, 0, self.ctx.particle_types.id_of("A")),
pr.Particle(1, 1, 1, self.ctx.particle_types.id_of("B"))]
self.model.get_particle_data().add_particles(particles)
self.ctx.configure()
def test_potential_order_2(self):
self.ctx.set_box_size(cmn.Vec(2, 2, 2))
self.ctx.periodic_boundary = [True, True, True]
self.model.get_particle_data().clear()
class MyPot2(pr.PotentialOrder2):
def __init__(self, typea, typeb):
super(MyPot2, self).__init__(typea, typeb)
def calculate_energy(self, x_ij):
return np.sqrt(x_ij * x_ij)
def calculate_force(self, x_ij):
return .5 * x_ij
def configure_for_types(self, type1, type2):
pass
def get_cutoff_radius(self):
return 5.0
def get_maximal_force(self, kbt):
return kbt
self.ctx.particle_types().add("A", 1.0, 1.0, 0)
self.ctx.particle_types().add("B", 1.0, 1.0, 0)
pot = MyPot2("A", "B")
self.ctx.potentials().add_external_order2(pot)
particles = [
pr.Particle(0, 0, 0,
self.ctx.particle_types().id_of("A")),
pr.Particle(1, 1, 1,
self.ctx.particle_types().id_of("B"))
]
add_particles_program = self.progs.create_add_particles(particles)
add_particles_program.perform()
self.ctx.configure()
self.progs.create_update_neighbor_list().perform()
self.progs.create_update_forces().perform()
np.testing.assert_almost_equal(self.model.get_energy(), np.sqrt(3))
it = self.model.get_particle_data().entries
entry = next(it)
if entry.type == self.ctx.particle_types().id_of("A"):
np.testing.assert_equal(entry.force, cmn.Vec(.5, .5, .5))
np.testing.assert_equal(next(it).force, cmn.Vec(-.5, -.5, -.5))
else:
np.testing.assert_equal(entry.force, cmn.Vec(-.5, -.5, -.5))
np.testing.assert_equal(next(it).force, cmn.Vec(.5, .5, .5))
with np.testing.assert_raises(StopIteration):
next(it)
def test_potential_order_1(self):
self.ctx.box_size = [2., 2., 2.]
self.ctx.pbc = [True, True, True]
self.model.get_particle_data().clear()
class MyPot1(pr.PotentialOrder1):
def __init__(self, type):
super(MyPot1, self).__init__(type)
def calculate_energy(self, pos_vec):
return 5.0
def calculate_force(self, pos_vec):
return cmn.Vec(.1, .1, .1)
def configure_for_type(self, type):
pass
def get_relevant_length_scale(self):
return 5.0
def get_maximal_force(self, kbt):
return kbt
self.ctx.particle_types.add("A", 1.0, 0)
pot = MyPot1(self.ctx.particle_types.id_of("A"))
self.ctx.potentials.add_external_order1(pot)
particles = [pr.Particle(0, 0, .5, self.ctx.particle_types.id_of("A"))]
self.model.get_particle_data().add_particles(particles)
self.ctx.configure()
def test_factory_programs(self):
kernel = pr.SingleCPUKernel()
kernel.get_kernel_context().particle_types().add("A", 1.0, 1.0)
factory = kernel.get_action_factory()
add_particles = factory.create_add_particles([pr.Particle(0, 0, 0, 0), pr.Particle(1, 1, 1, 0)])
integrator = factory.create_euler_integrator(1)
forces = factory.create_update_forces()
neighbor_list = factory.create_update_neighbor_list()
reactions = factory.create_reactions_uncontrolled_approximation(1)
add_particles.perform()
state_model = kernel.get_kernel_state_model()
positions = state_model.get_particle_positions()
np.testing.assert_equal(positions[0], cmn.Vec(0, 0, 0))
np.testing.assert_equal(positions[1], cmn.Vec(1, 1, 1))
it = kernel.get_kernel_state_model().get_particle_data().entries
assert next(it).pos == cmn.Vec(0, 0, 0)
assert next(it).pos == cmn.Vec(1, 1, 1)
with np.testing.assert_raises(StopIteration):
next(it)
def test_potential_order_1(self):
self.ctx.set_box_size(cmn.Vec(2, 2, 2))
self.ctx.periodic_boundary = [True, True, True]
self.model.get_particle_data().clear()
class MyPot1(pr.PotentialOrder1):
def __init__(self, type):
super(MyPot1, self).__init__(type)
def calculate_energy(self, pos_vec):
return 5.0
def calculate_force(self, pos_vec):
return cmn.Vec(.1, .1, .1)
def configure_for_type(self, type):
pass
def get_relevant_length_scale(self):
return 5.0
def get_maximal_force(self, kbt):
return kbt
self.ctx.particle_types().add("A", 1.0, 1.0, 0)
pot = MyPot1("A")
self.ctx.potentials().add_external_order1(pot)
particles = [
pr.Particle(0, 0, .5,
self.ctx.particle_types().id_of("A"))
]
add_particles_program = self.progs.create_add_particles(particles)
add_particles_program.perform()
self.ctx.configure()
updforces = self.progs.create_update_forces()
updforces.perform()
np.testing.assert_equal(
self.model.get_energy(),
5.0,
err_msg="the user defined potential returns energy=5.0")
data = self.model.get_particle_data()
it = data.entries
f_vec = next(it).force
np.testing.assert_equal(f_vec, cmn.Vec(.1, .1, .1))
with np.testing.assert_raises(StopIteration):
next(it)