def test_distribute_scalar(self):
a = self.Array(MeshGrid(1, 2))
a.distribute_at_positions(8, self.xp.full((1000, 3), 0.5))
assert_array_equal(a.data, np.full((2, 2, 2), 1000))
a.distribute_at_positions(8, self.xp.full((1000, 3), 0.5))
assert_array_equal(a.data, np.full((2, 2, 2), 2000))
a.reset()
a.distribute_at_positions(1, self.xp.full((1000, 3), 0.1))
assert_array_almost_equal(
a.data, np.array([[[729, 81], [81, 9]], [[81, 9], [9, 1]]]))
a = self.Array(MeshGrid((2, 4, 8), (3, 3, 3)))
a.distribute_at_positions(-2, [(1, 1, 3)])
assert_array_equal(
a.data, [[[0, 0, 0], [0, 0, 0], [0, 0, 0]],
[[-0.25 / 8, -0.75 / 8, 0], [-0.25 / 8, -0.75 / 8, 0],
[0, 0, 0]], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]])
a.reset()
a.distribute_at_positions(-2, [(1, 1, 3), (1, 1, 3)])
assert_array_equal(
a.data, [[[0, 0, 0], [0, 0, 0], [0, 0, 0]],
[[-0.25 / 4, -0.75 / 4, 0], [-0.25 / 4, -0.75 / 4, 0],
[0, 0, 0]], [[0, 0, 0], [0, 0, 0], [0, 0, 0]]])
a.reset()
a.distribute_at_positions(-2, [(2, 4, 8)])
assert_array_equal(a.data, [[[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, -0.25]]])
a.reset()
def test_interpolate_scalar(self):
a = self.Array(MeshGrid(1, 2), None,
[[[0, 1], [0, -1]], [[0, 0], [0, 0]]])
positions = np.array([(0, 0, 0), (0, 0, 1), (0, 1, 0), (0, 1, 1),
(1, 0, 0), (1, 0, 1), (1, 1, 0), (1, 1, 1),
(0.5, 0.5, 0.5), (0.5, 0, 0.5), (0.5, 1, 0.5),
(0, 0, 2)],
dtype=float)
assert_array_equal(a.interpolate_at_positions(positions),
[0, 1, 0, -1, 0, 0, 0, 0, 0, 0.25, -0.25, 0])
assert_array_equal(a.interpolate_at_positions(positions[1:2]), [1.])
a = self.Array(
MeshGrid((100, 20, 100), (101, 44, 101)), None,
np.arange(101 * 44 * 101, dtype=float).reshape((101, 44, 101)))
positions = np.linspace((0, 13, 100.1), (100.1, 0, 0), 314)
o, s = np.zeros(3), np.array([100, 20, 100])
xyz = tuple(
np.linspace(o[i], o[i] + s[i], a.n_nodes[i]) for i in (0, 1, 2))
interpolator = RegularGridInterpolator(xyz,
a.data,
bounds_error=False,
fill_value=0)
r1 = a.interpolate_at_positions(self.xp.asarray(positions))
assert_array_almost_equal(r1, interpolator(positions))
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_init(self):
a = self.Array(MeshGrid(10, 11))
assert a.value_shape == ()
assert_array_equal(a.data, np.zeros([11] * 3))
assert type(a._data) == self.xp.ndarray
data = self.xp.ones((5, 5, 5, 3))
a = self.Array(MeshGrid(1, 5), 3, data)
assert a.value_shape == (3, )
assert_array_equal(a.data, np.ones((5, 5, 5, 3)))
assert type(a._data) == self.xp.ndarray
assert a._data is not data # data gets copied don't create ArrayOnGrid every cycle
with raises(ValueError):
self.Array(MeshGrid(1, 5), data=self.xp.ones((5, 5, 5, 3)))
def test_do_init_warnings(self, capsys, caplog):
MeshGrid.from_step((12, 12, 12), (5, 5, 7))
out, err = capsys.readouterr()
assert out == ""
assert err == ""
assert caplog.record_tuples == [
('root', logging.WARNING,
"X step on spatial grid was reduced to 4.000 from 5.000 to fit in a round number of cells."
),
('root', logging.WARNING,
"Y step on spatial grid was reduced to 4.000 from 5.000 to fit in a round number of cells."
),
('root', logging.WARNING,
"Z step on spatial grid was reduced to 6.000 from 7.000 to fit in a round number of cells."
),
]
def test_node_coordinates(self):
coords = np.array([[[[0., 0., 0.], [0., 0., 3.]],
[[0., 1., 0.], [0., 1., 3.]],
[[0., 2., 0.], [0., 2., 3.]]],
[[[2., 0., 0.], [2., 0., 3.]],
[[2., 1., 0.], [2., 1., 3.]],
[[2., 2., 0.], [2., 2., 3.]]],
[[[4., 0., 0.], [4., 0., 3.]],
[[4., 1., 0.], [4., 1., 3.]],
[[4., 2., 0.], [4., 2., 3.]]]])
assert_array_equal(
MeshGrid.from_step((4, 2, 3), (2, 1, 3)).node_coordinates, coords)
assert_array_equal(
MeshGrid.from_step((4, 2, 3), (2, 1, 3),
(1, 2, 3.14)).node_coordinates,
coords + [1, 2, 3.14])
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_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 __init__(self,
name,
electric_or_magnetic,
field_filename,
xp=numpy,
array_class=ArrayOnGrid):
if not os.path.exists(field_filename):
raise FileNotFoundError("Field file not found")
raw = numpy.loadtxt(field_filename, skiprows=1)
# assume X Y Z Fx Fy Fz columns
# sort by column 0, then 1, then 2
# https://stackoverflow.com/a/38194077
ind = raw[:, 2].argsort() # First sort doesn't need to be stable.
raw = raw[ind]
ind = raw[:, 1].argsort(kind='mergesort')
raw = raw[ind]
ind = raw[:, 0].argsort(kind='mergesort')
raw = raw[ind]
size = (raw[-1, :3] - raw[0, :3])
origin = raw[0, :3]
dist = raw[:, :3] - raw[0, :3]
step = dist.min(axis=0, where=dist > 0, initial=dist.max())
grid = MeshGrid.from_step(size, step, origin)
field = xp.asarray(raw[:, 3:].reshape((*grid.n_nodes, 3)))
super().__init__(name, electric_or_magnetic,
array_class(grid, 3, field))
self.field_filename = field_filename
def test_distribute_vector(self):
a = self.Array(MeshGrid(1, 2))
with raises(
ValueError,
match="operands could not be broadcast together with shapes"):
a.distribute_at_positions(self.xp.array([8, 8, 8]),
self.xp.full((1000, 3), 0.5))
def test_all_config(self, backend):
efconf = Config(
TimeGridConf(200, 20, 2),
SpatialMeshConf((5, 5, 5), (.1, .1, .1)),
sources=[
ParticleSourceConf('a', Box()),
ParticleSourceConf('c', Cylinder()),
ParticleSourceConf('d', Tube(start=(0, 0, 0), end=(0, 0, 1)))
],
inner_regions=[
InnerRegionConf('1', Box(), 1),
InnerRegionConf('2', Sphere(), -2),
InnerRegionConf('3', Cylinder(), 0),
InnerRegionConf('4', Tube(), 4)
],
output_file=OutputFileConf(),
boundary_conditions=BoundaryConditionsConf(-2.7),
particle_interaction_model=ParticleInteractionModelConf('binary'),
external_fields=[
ExternalElectricFieldUniformConf('x', (-2, -2, 1)),
ExternalMagneticFieldExpressionConf(
'y', ('0', '0', '3*x + sqrt(y) - z**2'))
])
parser = ConfigParser()
parser.read_string(efconf.export_to_string())
conf = Config.from_configparser(parser)
sim = conf.make()
assert_dataclass_eq(sim.time_grid, TimeGrid(200, 2, 20))
assert_dataclass_eq(sim.mesh, MeshGrid(5, 51))
assert_dataclass_eq(
sim.electric_field,
FieldOnGrid('spatial_mesh', 'electric', self.Array(sim.mesh, 3)))
assert_dataclass_eq(sim.charge_density, self.Array(sim.mesh))
expected = np.full((51, 51, 51), -2.7)
expected[1:-1, 1:-1, 1:-1] = 0
assert_dataclass_eq(sim.potential, self.Array(sim.mesh, (), expected))
_assert_value_eq(sim.inner_regions, [
InnerRegion('1', Box(), 1),
InnerRegion('2', Sphere(), -2),
InnerRegion('3', Cylinder(), 0),
InnerRegion('4', Tube(), 4)
])
_assert_value_eq(sim.particle_sources, [
ParticleSourceConf('a', Box()).make(),
ParticleSourceConf('c', Cylinder()).make(),
ParticleSourceConf('d', Tube(start=(0, 0, 0),
end=(0, 0, 1))).make()
])
assert_dataclass_eq(
sim.electric_fields,
FieldUniform('x', 'electric', np.array((-2, -2, 1))))
assert_dataclass_eq(
sim.magnetic_fields,
FieldExpression('y', 'magnetic', '0', '0', '3*x + sqrt(y) - z**2'))
assert sim.particle_interaction_model == Model.binary
def test_do_init(self):
a = ArrayOnGrid(MeshGrid.from_step((12, 12, 12), (4, 4, 6)))
a.apply_boundary_values(BoundaryConditionsConf(1, 2, 3, 4, 5, 6))
expected = np.array([[[5., 1., 6.], [5., 1., 6.], [5., 1., 6.],
[5., 1., 6.]],
[[5., 3., 6.], [5., 0., 6.], [5., 0., 6.],
[5., 4., 6.]],
[[5., 3., 6.], [5., 0., 6.], [5., 0., 6.],
[5., 4., 6.]],
[[5., 2., 6.], [5., 2., 6.], [5., 2., 6.],
[5., 2., 6.]]])
assert_array_equal(a.data, expected)
def test_interpolate_vector(self):
a = self.Array(MeshGrid((2, 4, 8), (3, 3, 3)), 3,
self.xp.full((3, 3, 3, 3), 100))
a._data[1:2, 0:2, 0:2] = self.xp.array([[[2, 1, 0], [-3, 1, 0]],
[[0, -1, 0], [-1, 0, 0]]])
assert_array_equal(
a.interpolate_at_positions(np.array([(1, 1, 3)], dtype=float)),
[(-1.25, 0.375, 0)])
assert_array_equal(
a.interpolate_at_positions(
self.xp.array([(1, 1, 3), (2, 1, 3), (1.5, 1, 3)],
dtype=float)), [(-1.25, 0.375, 0),
(100, 100, 100),
(49.375, 50.1875, 50)])
def test_n_nodes(self):
assert self.Array(MeshGrid(10, 11)).n_nodes == (11, 11, 11)
assert self.Array(MeshGrid(10, 11), None).n_nodes == (11, 11, 11)
assert self.Array(MeshGrid(10, 11), ()).n_nodes == (11, 11, 11)
assert self.Array(MeshGrid(10, 11),
1).n_nodes == (11, 11, 11, 1) # Should this be true?
assert self.Array(MeshGrid(10, 11), 3).n_nodes == (11, 11, 11, 3)
assert self.Array(MeshGrid(10, 11),
(2, 5)).n_nodes == (11, 11, 11, 2, 5)
def test_transfer_solution_to_spat_mesh(self):
mesh = MeshGrid.from_step((4, 6, 9), (1, 2, 3))
solver = FieldSolver(mesh, [])
solver.phi_vec = np.array(range(1, 3 * 2 * 2 + 1))
potential = ArrayOnGrid(mesh)
solver.transfer_solution_to_spat_mesh(potential)
assert_array_equal(
potential.data[1:-1, 1:-1, 1:-1],
[[[1, 7], [4, 10]], [[2, 8], [5, 11]], [[3, 9], [6, 12]]])
assert_array_equal(
potential.data,
[[[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0]],
[[0, 0, 0, 0], [0, 1, 7, 0], [0, 4, 10, 0], [0, 0, 0, 0]],
[[0, 0, 0, 0], [0, 2, 8, 0], [0, 5, 11, 0], [0, 0, 0, 0]],
[[0, 0, 0, 0], [0, 3, 9, 0], [0, 6, 12, 0], [0, 0, 0, 0]],
[[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0]]])
def test_init_from_config(self, backend):
efconf = Config()
parser = ConfigParser()
parser.read_string(efconf.export_to_string())
sim = Config.from_configparser(parser).make()
assert_dataclass_eq(sim.time_grid, TimeGrid(100, 1, 10))
g = MeshGrid(10, 11)
assert_dataclass_eq(sim.mesh, g)
assert_dataclass_eq(sim.potential, self.Array(g))
assert_dataclass_eq(sim.charge_density, self.Array(g))
assert_dataclass_eq(
sim.electric_field,
FieldOnGrid('spatial_mesh', 'electric', self.Array(g, 3)))
assert sim.inner_regions == []
assert sim.particle_sources == []
assert_dataclass_eq(sim.electric_fields,
FieldZero('ZeroSum', 'electric'))
assert_dataclass_eq(sim.magnetic_fields,
FieldZero('ZeroSum', 'magnetic'))
assert sim.particle_interaction_model == Model.PIC
def sim_full():
return Simulation(
TimeGrid(200, 2, 20),
MeshGrid(5, 51),
particle_sources=[
ParticleSource('a', Box()),
ParticleSource('c', Cylinder()),
ParticleSource('d', Tube(start=(0, 0, 0), end=(0, 0, 1)))
],
inner_regions=[
InnerRegion('1', Box(), 1),
InnerRegion('2', Sphere(), -2),
InnerRegion('3', Cylinder(), 0),
InnerRegion('4', Tube(), 4)
],
particle_interaction_model=Model.binary,
electric_fields=[FieldUniform('x', 'electric', (-2, -2, 1))],
magnetic_fields=[
FieldExpression('y', 'magnetic', '0', '0', '3*x + sqrt(y) - z**2')
])
def test_construct_equation_matrix(self):
mesh = MeshGrid.from_step((4, 6, 9), (1, 2, 3))
solver = FieldSolver(mesh, [])
solver.construct_equation_matrix()
d = -2 * (2 * 2 * 3 * 3 + 3 * 3 + 2 * 2)
x = 2 * 2 * 3 * 3
y = 3 * 3
z = 2 * 2
assert_array_equal(solver.A.toarray(),
[[d, x, 0, y, 0, 0, z, 0, 0, 0, 0, 0],
[x, d, x, 0, y, 0, 0, z, 0, 0, 0, 0],
[0, x, d, 0, 0, y, 0, 0, z, 0, 0, 0],
[y, 0, 0, d, x, 0, 0, 0, 0, z, 0, 0],
[0, y, 0, x, d, x, 0, 0, 0, 0, z, 0],
[0, 0, y, 0, x, d, 0, 0, 0, 0, 0, z],
[z, 0, 0, 0, 0, 0, d, x, 0, y, 0, 0],
[0, z, 0, 0, 0, 0, x, d, x, 0, y, 0],
[0, 0, z, 0, 0, 0, 0, x, d, 0, 0, y],
[0, 0, 0, z, 0, 0, y, 0, 0, d, x, 0],
[0, 0, 0, 0, z, 0, 0, y, 0, x, d, x],
[0, 0, 0, 0, 0, z, 0, 0, y, 0, x, d]])
def test_is_the_same_on_all_boundaries(self):
mesh = MeshGrid(12, (4, 4, 3))
a = self.Array(mesh)
assert a.is_the_same_on_all_boundaries
for x, y, z in np.ndindex(4, 4, 3):
a._data[x, y, z] = 2.
if 0 < x < 3 and 0 < y < 3 and 0 < z < 2:
assert a.is_the_same_on_all_boundaries
else:
assert not a.is_the_same_on_all_boundaries
a.reset()
assert a.is_the_same_on_all_boundaries
a = self.Array(mesh, 3)
assert a.is_the_same_on_all_boundaries
for x, y, z, t in np.ndindex(4, 4, 3, 3):
a._data[x, y, z, t] = 2.
if 0 < x < 3 and 0 < y < 3 and 0 < z < 2:
assert a.is_the_same_on_all_boundaries
else:
assert not a.is_the_same_on_all_boundaries
a.reset()
assert a.is_the_same_on_all_boundaries
def import_from_h5(h5file: h5py.File) -> Simulation:
fields = [Field.import_h5(g) for g in h5file['ExternalFields'].values()]
sources = [ParticleSource.import_h5(g) for g in h5file['ParticleSources'].values()]
particles = [ParticleArray.import_h5(g) for g in h5file['ParticleSources'].values()]
# cupy max has no `initial` argument
max_id = int(max([(p.ids.get() if hasattr(p.ids, 'get') else p.ids).max(initial=-1) for p in particles], default=-1))
g = h5file['SpatialMesh']
mesh = MeshGrid.import_h5(g)
charge = Reader.array_class(mesh, (), np.reshape(g['charge_density'], mesh.n_nodes))
potential = Reader.array_class(mesh, (), np.reshape(g['potential'], mesh.n_nodes))
field = FieldOnGrid('spatial_mesh', 'electric', Reader.array_class(mesh, 3, np.moveaxis(
np.array([np.reshape(g[f'electric_field_{c}'], mesh.n_nodes) for c in 'xyz']),
0, -1)))
return Simulation(
time_grid=TimeGrid.import_h5(h5file['TimeGrid']),
mesh=mesh, charge_density=charge, potential=potential, electric_field=field,
inner_regions=[InnerRegion.import_h5(g) for g in h5file['InnerRegions'].values()],
electric_fields=[f for f in fields if f.electric_or_magnetic == 'electric'],
magnetic_fields=[f for f in fields if f.electric_or_magnetic == 'magnetic'],
particle_interaction_model=Model[
h5file['ParticleInteractionModel'].attrs['particle_interaction_model'].decode('utf8')
],
particle_sources=sources, particle_arrays=particles, particle_tracker=ParticleTracker(max_id)
)
def test_gradient(self):
m = MeshGrid((1.5, 2, 1), (4, 3, 2))
potential = self.Array(m)
potential._data = self.xp.stack([
self.xp.array([[0., 0, 0], [1, 2, 3], [4, 3, 2], [4, 4, 4]]),
self.xp.zeros((4, 3))
], -1)
expected = self.Array(
m, 3, [[[[-2, 0, 0], [0, 0, 0]], [[-4, 0, 0], [0, 0, 0]],
[[-6, 0, 0], [0, 0, 0]]],
[[[-4, -1, 1], [0, 0, 1]], [[-3, -1, 2], [0, 0, 2]],
[[-2, -1, 3], [0, 0, 3]]],
[[[-3, 1, 4], [0, 0, 4]], [[-2, 1, 3], [0, 0, 3]],
[[-1, 1, 2], [0, 0, 2]]],
[[[0, 0, 4], [0, 0, 4]], [[-2, 0, 4], [0, 0, 4]],
[[-4, 0, 4], [0, 0, 4]]]])
field = potential.gradient()
assert_dataclass_eq(field, expected)
with raises(
ValueError,
match=
"Trying got compute gradient for a non-scalar field: ambiguous"
):
field.gradient()
def test_on_grid(self, backend):
f = FieldOnGrid('f1', 'electric',
inject.instance(ArrayOnGrid)(MeshGrid(5, 6), 3, inject.instance(np).full((6, 6, 6, 3), -3.14)))
assert_array_almost_equal(f.get_at_points([(-1, 0, 0), (1, 2, 3.5)], 1), [(0, 0, 0), (-3.14, -3.14, -3.14)])
with raises(ValueError):
FieldOnGrid('f1', 'electric', inject.instance(ArrayOnGrid)(MeshGrid(5, 6)))
def test_init(self):
m = MeshGrid(10, 11)
assert_array_equal(m.size, (10, 10, 10))
assert_array_equal(m.n_nodes, (11, 11, 11))
assert_array_equal(m.origin, (0, 0, 0))
def test_from_step(self):
assert_dataclass_eq(MeshGrid.from_step(10, 1, 7), MeshGrid(10, 11, 7))
assert_dataclass_eq(MeshGrid.from_step([10, 20, 5], [1, 4, 1]),
MeshGrid([10, 20, 5], [11, 6, 6]))
assert_dataclass_eq(MeshGrid.from_step(10, [1, 2, 4]),
MeshGrid(10, [11, 6, 4]))
def test_cell(self):
assert_array_equal(MeshGrid(10, 11, 7).cell, (1, 1, 1))
assert_array_equal(
MeshGrid.from_step(10, [1, 2, 4]).cell, [1, 2, 10 / 3])
def test_do_init_ranges(self):
with raises(ValueError):
MeshGrid.from_step((10, 20), (2, 1, 3))
with raises(ValueError):
MeshGrid.from_step(((1, 2), 3), (1, 1, 1))
with raises(ValueError):
MeshGrid.from_step((10, 10, 10), [[2, 1, 3], [4, 5, 6], [7, 8, 9]],
BoundaryConditionsConf(3.14))
with raises(ValueError):
MeshGrid.from_step((10, 10, -30), (2, 1, 3))
with raises(ValueError):
MeshGrid.from_step((10, 10, 10), (2, -2, 3))
mesh = MeshGrid.from_step((10, 10, 10), (17, 2, 3))
assert tuple(mesh.cell) == (10, 2, 2.5)
def test_zero(self):
z = self.Array(MeshGrid(10, 5), (2, 5)).zero
assert type(z) == self.xp.ndarray
assert z.shape == (5, 5, 5, 2, 5)
assert (z == 0).all()
def test_reset(self):
a = self.Array(MeshGrid(1, 5), (), self.xp.ones((5, 5, 5)))
assert_array_equal(a.data, np.ones((5, 5, 5)))
a.reset()
assert_array_equal(a.data, np.zeros((5, 5, 5)))
