def test_init(self):
ir = InnerRegion('test', Box())
assert ir.name == 'test'
assert_dataclass_eq(ir.shape, Box())
assert ir.total_absorbed_particles == 0
assert ir.total_absorbed_charge == 0
assert ir.inverted == False
def test_absorb_charge_inverted(self):
particles = ParticleArray([1], -2.0, 1.0, (0, 0, 0), np.zeros(3))
ir = InnerRegion('test', Box(), inverted=True)
assert ir.total_absorbed_particles == 0
assert ir.total_absorbed_charge == 0
ir.collide_with_particles(particles)
assert ir.total_absorbed_particles == 0
assert ir.total_absorbed_charge == 0
assert_dataclass_eq(
particles,
ParticleArray([1], -2.0, 1.0, np.zeros((1, 3)), np.zeros((1, 3))))
particles = ParticleArray([1], -2.0, 1.0, (10, 10, 10), np.zeros(3))
ir = InnerRegion('test', Box(), inverted=True)
assert ir.total_absorbed_particles == 0
assert ir.total_absorbed_charge == 0
ir.collide_with_particles(particles)
assert ir.total_absorbed_particles == 1
assert ir.total_absorbed_charge == -2
assert_dataclass_eq(
particles,
ParticleArray([], -2.0, 1.0, np.zeros((0, 3)), np.zeros((0, 3))))
particles = ParticleArray([1, 2], -2.0, 1.0, [(0, 0, 0), (10, 10, 10)],
np.zeros((2, 3)))
ir = InnerRegion('test', Box(), inverted=True)
assert ir.total_absorbed_particles == 0
assert ir.total_absorbed_charge == 0
ir.collide_with_particles(particles)
assert ir.total_absorbed_particles == 1
assert ir.total_absorbed_charge == -2
assert_dataclass_eq(
particles,
ParticleArray([1], -2.0, 1.0, [(0, 0, 0)], np.zeros((1, 3))))
def test_absorb_charge(self):
particles = ParticleArray([1], -2.0, 1.0, (0, 0, 0), np.zeros(3))
ir = InnerRegion('test', Box())
assert ir.total_absorbed_particles == 0
assert ir.total_absorbed_charge == 0
ir.collide_with_particles(particles)
assert ir.total_absorbed_particles == 1
assert ir.total_absorbed_charge == -2
assert particles == ParticleArray([], -2.0, 1.0, np.zeros((0, 3)), np.zeros((0, 3)))
particles = ParticleArray([1], -2.0, 1.0, (10, 10, 10), np.zeros(3))
ir = InnerRegion('test', Box())
assert ir.total_absorbed_particles == 0
assert ir.total_absorbed_charge == 0
ir.collide_with_particles(particles)
assert ir.total_absorbed_particles == 0
assert ir.total_absorbed_charge == 0
assert particles == ParticleArray([1], -2.0, 1.0, [(10, 10, 10)], np.zeros((1, 3)))
particles = ParticleArray([1, 2], -2.0, 1.0, [(0, 0, 0), (10, 10, 10)], np.zeros((2, 3)))
ir = InnerRegion('test', Box())
assert ir.total_absorbed_particles == 0
assert ir.total_absorbed_charge == 0
ir.collide_with_particles(particles)
assert ir.total_absorbed_particles == 1
assert ir.total_absorbed_charge == -2
assert particles == ParticleArray([2], -2.0, 1.0, [(10, 10, 10)], np.zeros((1, 3)))
def test_zero_nondiag_inside_objects(self, backend):
mesh = MeshGrid.from_step((4, 6, 9), (1, 2, 3))
solver = FieldSolver(
mesh, [InnerRegion('test', Box((1, 2, 3), (1, 2, 3)), 3)])
a = scipy.sparse.coo_matrix(np.full((12, 12), 2))
assert_array_equal(a.toarray(), [[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]])
result = solver.zero_nondiag_for_nodes_inside_objects(a)
assert_array_equal(result.toarray(),
[[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]])
a = scipy.sparse.coo_matrix(
np.array([[4, 0, 3, 0, 0, 0, 0, 2, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 4, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 2, 0, 0, 3, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 2, 0, 0, 0, 0, 0, 0, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 6, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]))
result = solver.zero_nondiag_for_nodes_inside_objects(a)
assert_array_equal(result.toarray(),
[[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 2, 0, 0, 3, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
def test_generate_nodes_in_regions(self, backend):
mesh = MeshGrid.from_step((4, 6, 9), (1, 2, 3))
solver = FieldSolver(mesh, [])
inner_regions = [InnerRegion('test', Box((1, 2, 3), (1, 2, 3)), 3)]
nodes, potential = solver.generate_nodes_in_regions(inner_regions)
assert_array_equal(nodes, [0, 1, 3, 4, 6, 7, 9, 10])
assert_array_equal(potential, [3, 3, 3, 3, 3, 3, 3, 3])
def test_particle_ids(self):
p1 = ParticleSource("test", Box(), 120, 5, np.array((1, 0, 0)), 200,
-1, 2)
a1 = p1.generate_initial_particles()
a2 = p1.generate_each_step()
assert_array_equal(a1.ids, range(120))
assert_array_equal(a2.ids, range(5))
def test_init_rhs(self, backend):
mesh = MeshGrid.from_step((4, 3, 3), 1)
solver = FieldSolver(mesh, [])
solver.init_rhs_vector_in_full_domain(ArrayOnGrid(mesh),
ArrayOnGrid(mesh))
assert_array_equal(solver.rhs, np.zeros(3 * 2 * 2))
pot = ArrayOnGrid(mesh)
pot.apply_boundary_values(BoundaryConditionsConf(-2))
solver.init_rhs_vector_in_full_domain(ArrayOnGrid(mesh), pot)
assert_array_equal(solver.rhs,
[6, 4, 6, 6, 4, 6, 6, 4, 6, 6, 4, 6]) # what
del solver
mesh = MeshGrid.from_step((4, 4, 5), 1)
pot = ArrayOnGrid(mesh)
pot.apply_boundary_values(BoundaryConditionsConf(-2))
solver = FieldSolver(mesh, [])
solver.init_rhs_vector_in_full_domain(ArrayOnGrid(mesh), pot)
assert_array_equal(solver.rhs, [
6, 4, 6, 4, 2, 4, 6, 4, 6, 4, 2, 4, 2, 0, 2, 4, 2, 4, 4, 2, 4, 2,
0, 2, 4, 2, 4, 6, 4, 6, 4, 2, 4, 6, 4, 6
]) # what
del solver
mesh = MeshGrid.from_step((8, 12, 5), (2, 3, 1))
pot = ArrayOnGrid(mesh)
pot.apply_boundary_values(BoundaryConditionsConf(-1))
solver = FieldSolver(mesh, [])
solver.init_rhs_vector_in_full_domain(ArrayOnGrid(mesh), pot)
assert_array_equal(solver.rhs, [
49, 40, 49, 45, 36, 45, 49, 40, 49, 13, 4, 13, 9, 0, 9, 13, 4, 13,
13, 4, 13, 9, 0, 9, 13, 4, 13, 49, 40, 49, 45, 36, 45, 49, 40, 49
])
del solver
mesh = MeshGrid.from_step((4, 6, 9), (1, 2, 3))
charge = ArrayOnGrid(mesh)
charge._data = np.array([[[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0],
[0, 0, 0, 0]],
[[0, 0, 0, 0], [0, 1, 2, 0], [0, -1, 0, 0],
[0, 0, 0, 0]],
[[0, 0, 0, 0], [0, 3, 4, 0], [0, 0, -1, 0],
[0, 0, 0, 0]],
[[0, 0, 0, 0], [0, 5, 6, 0], [0, -1, 0, 0],
[0, 0, 0, 0]],
[[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0],
[0, 0, 0, 0]]])
solver = FieldSolver(mesh, [])
solver.init_rhs_vector_in_full_domain(charge, ArrayOnGrid(mesh))
assert_allclose(
solver.rhs, -np.array([1, 3, 5, -1, 0, -1, 2, 4, 6, 0, -1, 0]) *
np.pi * 4 * 36)
solver = FieldSolver(mesh, [])
nodep = solver.generate_nodes_in_regions(
[InnerRegion('test', Box((1, 2, 3), (1, 2, 3)), 3)])
solver.nodes_in_regions, solver.potential_in_regions = nodep
solver.init_rhs_vector(ArrayOnGrid(mesh), ArrayOnGrid(mesh))
assert_array_equal(solver.rhs, [3, 3, 0, 3, 3, 0, 3, 3, 0, 3, 3, 0])
def test_generate(self):
p1 = ParticleSource("test", Box(), 120, 5, np.array((1, 0, 0)), 200,
-1, 2)
p2 = ParticleSource("test", Box(), 120, 5, np.array((1, 0, 0)), 200,
-1, 2)
p3 = ParticleSource("test", Box(), 120, 5, np.array((1, 0, 0)), 200,
-1, 2)
p3._generator.set_state(p1._generator.get_state())
a1 = p1.generate_initial_particles()
a2 = p2.generate_initial_particles()
a3 = p3.generate_initial_particles()
assert a1 != a2
assert a1 == a3
a32 = p3.generate_each_step()
assert a1 != a32
a12 = p1.generate_each_step()
assert a12 == a32
def test_generate_positions(self):
ps = ParticleSource()
ps._generator = RandomState(123)
p = ps.generate_num_of_particles(100)
assert_ae = p.xp.testing.assert_array_equal
assert_ae(
p.positions,
Box().generate_uniform_random_posititons(RandomState(123), 100))
def test_h5(self, tmpdir):
fname = tmpdir.join('test_particle_source.h5')
p1 = ParticleSource("test", Box(), 120, 5, np.array((1, 0, 0)), 0, -1,
2)
with h5py.File(fname, mode="w") as h5file:
p1.save_h5(h5file)
with h5py.File(fname, mode="r") as h5file:
p2 = ParticleSource.load_h5(h5file)
assert p1 == p2
def test_generate_for_simulation(self):
ps = ParticleSource('test', Box(6, 0), 17, 13, (4, 4, 4), 0, -2, 6)
assert_dataclass_eq(
ps.generate_initial_particles(),
ParticleArray(range(17), -2, 6, np.full((17, 3), 6),
np.full((17, 3), 4), False))
assert_dataclass_eq(
ps.generate_each_step(),
ParticleArray(range(13), -2, 6, np.full((13, 3), 6),
np.full((13, 3), 4), False))
def test_init(self):
p = ParticleSource()
assert p.name == "particle_source"
assert_dataclass_eq(p.shape, Box())
assert p.initial_number_of_particles == 0
assert p.particles_to_generate_each_step == 0
assert_array_equal(p.mean_momentum, np.zeros(3))
assert p.temperature == 0
assert p.charge == 0
assert p.mass == 1
def test_init_rhs(self):
mesh = SpatialMeshConf((4, 3, 3)).make(BoundaryConditionsConf())
solver = FieldSolver(mesh, [])
solver.init_rhs_vector_in_full_domain(mesh)
assert_array_equal(solver.rhs, np.zeros(3 * 2 * 2))
mesh = SpatialMeshConf((4, 3, 3)).make(BoundaryConditionsConf(-2))
solver = FieldSolver(mesh, [])
solver.init_rhs_vector_in_full_domain(mesh)
assert_array_equal(solver.rhs,
[6, 4, 6, 6, 4, 6, 6, 4, 6, 6, 4, 6]) # what
mesh = SpatialMeshConf((4, 4, 5)).make(BoundaryConditionsConf(-2))
solver = FieldSolver(mesh, [])
solver.init_rhs_vector_in_full_domain(mesh)
assert_array_equal(solver.rhs, [
6, 4, 6, 4, 2, 4, 6, 4, 6, 4, 2, 4, 2, 0, 2, 4, 2, 4, 4, 2, 4, 2,
0, 2, 4, 2, 4, 6, 4, 6, 4, 2, 4, 6, 4, 6
]) # what
mesh = SpatialMeshConf((8, 12, 5),
(2, 3, 1)).make(BoundaryConditionsConf(-1))
solver = FieldSolver(mesh, [])
solver.init_rhs_vector_in_full_domain(mesh)
assert_array_equal(solver.rhs, [
49, 40, 49, 45, 36, 45, 49, 40, 49, 13, 4, 13, 9, 0, 9, 13, 4, 13,
13, 4, 13, 9, 0, 9, 13, 4, 13, 49, 40, 49, 45, 36, 45, 49, 40, 49
])
mesh = SpatialMeshConf((4, 6, 9),
(1, 2, 3)).make(BoundaryConditionsConf())
solver = FieldSolver(mesh, [])
mesh.charge_density = np.array([[[0, 0, 0, 0], [0, 0, 0, 0],
[0, 0, 0, 0], [0, 0, 0, 0]],
[[0, 0, 0, 0], [0, 1, 2, 0],
[0, -1, 0, 0], [0, 0, 0, 0]],
[[0, 0, 0, 0], [0, 3, 4, 0],
[0, 0, -1, 0], [0, 0, 0, 0]],
[[0, 0, 0, 0], [0, 5, 6, 0],
[0, -1, 0, 0], [0, 0, 0, 0]],
[[0, 0, 0, 0], [0, 0, 0, 0],
[0, 0, 0, 0], [0, 0, 0, 0]]])
solver.init_rhs_vector_in_full_domain(mesh)
assert_allclose(
solver.rhs, -np.array([1, 3, 5, -1, 0, -1, 2, 4, 6, 0, -1, 0]) *
np.pi * 4 * 36)
mesh = SpatialMeshConf((4, 6, 9),
(1, 2, 3)).make(BoundaryConditionsConf())
solver = FieldSolver(mesh, [])
region = InnerRegion('test', Box((1, 2, 3), (1, 2, 3)), 3)
solver.init_rhs_vector(mesh, [region])
assert_array_equal(solver.rhs, [3, 3, 0, 3, 3, 0, 3, 3, 0, 3, 3, 0])
def test_generate_particles(self):
ps = ParticleSource('test', Box((1., 2., 3.), 0), 17, 13, (-2, 3, 1),
0, -2, 6)
assert_dataclass_eq(
ps.generate_num_of_particles(3),
ParticleArray(range(3), -2, 6, [(1, 2, 3)] * 3, [(-2, 3, 1)] * 3,
False))
assert_dataclass_eq(
ps.generate_num_of_particles(1),
ParticleArray([0], -2, 6, [(1, 2, 3)], [(-2, 3, 1)], False))
assert_dataclass_eq(
ps.generate_num_of_particles(0),
ParticleArray([], -2, 6, np.empty((0, 3)), np.empty((0, 3)),
False))
def test_zero_nondiag_inside_objects(self):
mesh = SpatialMeshConf((4, 6, 9),
(1, 2, 3)).make(BoundaryConditionsConf())
solver = FieldSolver(mesh, [])
region = InnerRegion('test', Box((1, 2, 3), (1, 2, 3)), 3)
a = csr_matrix(np.full((12, 12), 2))
assert_array_equal(a.toarray(), [[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]])
result = solver.zero_nondiag_for_nodes_inside_objects(
a, mesh, [region])
assert_array_equal(result.toarray(),
[[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0],
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]])
# TODO: check algorithm if on-diagonal zeros should turn into ones
a = csr_matrix(
np.array([[4, 0, 3, 0, 0, 0, 0, 2, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 4, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 2, 0, 0, 3, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 2, 0, 0, 0, 0, 0, 0, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 6, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]))
result = solver.zero_nondiag_for_nodes_inside_objects(
a, mesh, [region])
assert_array_equal(result.toarray(),
[[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 2, 0, 0, 3, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])