def test_binary_field(self):
d = Config().make()
d.particle_arrays = [ParticleArray(1, -1, 1, [(1, 2, 3)], [(-2, 2, 0)], False)]
assert_array_almost_equal(d.binary_electric_field_at_positions((1, 2, 3)), (0, 0, 0))
assert_array_almost_equal(d.binary_electric_field_at_positions((1, 2, 4)), (0, 0, -1))
assert_array_almost_equal(d.binary_electric_field_at_positions((0, 2, 3)), (1, 0, 0))
assert_array_almost_equal(d.binary_electric_field_at_positions((0, 1, 2)), (1 / sqrt(27), 1 / sqrt(27), 1 / sqrt(27)))
def test_all_config(self):
efconf = Config(TimeGridConf(200, 20, 2), SpatialMeshConf((5, 5, 5), (.1, .1, .1)),
sources=[ParticleSourceConf('a', Box()),
ParticleSourceConf('c', Cylinder()),
ParticleSourceConf('d', Tube())],
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=[ExternalFieldUniformConf('x', 'electric', (-2, -2, 1)),
ExternalFieldExpressionConf('y', 'magnetic',
('0', '0', '3*x + sqrt(y) - z**2'))])
parser = ConfigParser()
parser.read_string(efconf.export_to_string())
sim = Config.from_configparser(parser).make()
assert sim.time_grid == TimeGrid(200, 2, 20)
assert sim.spat_mesh == SpatialMesh.do_init((5, 5, 5), (.1, .1, .1), BoundaryConditionsConf(-2.7))
assert sim.inner_regions == [InnerRegion('1', Box(), 1),
InnerRegion('2', Sphere(), -2),
InnerRegion('3', Cylinder(), 0),
InnerRegion('4', Tube(), 4)]
assert type(sim._field_solver) == FieldSolver
assert sim.particle_sources == [ParticleSourceConf('a', Box()).make(),
ParticleSourceConf('c', Cylinder()).make(),
ParticleSourceConf('d', Tube()).make()]
assert sim.electric_fields == [ExternalFieldUniform('x', 'electric', np.array((-2, -2, 1)))]
assert sim.magnetic_fields == [ExternalFieldExpression('y', 'magnetic', '0', '0', '3*x + sqrt(y) - z**2')]
assert sim.particle_interaction_model == ParticleInteractionModel("binary")
assert sim._output_filename_prefix == "out_"
assert sim._output_filename_suffix == ".h5"
def test_particle_generation(self, monkeypatch, tmpdir,
backend_and_solver):
monkeypatch.chdir(tmpdir)
conf = Config(
TimeGridConf(2, 1, 1),
SpatialMeshConf((5, 5, 5), (.1, .1, .1)),
sources=[
ParticleSourceConf('a',
Box((2, 2, 2), (0, 0, 0)),
2,
1, (0, 0, 0),
0,
charge=0),
ParticleSourceConf('b',
Box((1, 1, 1), (0, 0, 0)),
7,
5, (0, 0, 0),
0,
charge=0)
],
inner_regions=[InnerRegionConf('1', Box((.5, .5, .5), (1, 1, 1)))],
output_file=OutputFileConf(),
boundary_conditions=BoundaryConditionsConf(),
particle_interaction_model=ParticleInteractionModelConf(
'noninteracting'),
external_fields=[])
sim = conf.make()
Runner(sim).start()
assert [len(a.ids) for a in sim.particle_arrays] == [4]
def test_single_particle_in_free_space(tmpdir):
run_jupyter("examples/single_particle_in_free_space",
"single_particle_in_free_space.ipynb", tmpdir.join('newdir'),
True)
assert_dataclass_eq(
Config.from_fname(tmpdir.join('newdir').join('config.ini')),
Config.from_fname(
tmpdir.join('newdir').join('single_particle_in_free_space.conf')))
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_large_grid(solver_, backend_):
try:
configure_application(solver_, backend_)
c = Config(TimeGridConf(1, 1, 1), SpatialMeshConf(100, 1),
inner_regions=[InnerRegionConf('tube',
Tube((50, 50, 10), (50, 50, 12), 10, 90),
10)])
r = Runner(c.make())
r.eval_and_write_fields_without_particles()
assert r.simulation.potential.data.mean() >= 0
assert r.simulation.potential.data.mean() <= 10
assert abs(r.simulation.potential.data.max() - 10) < 0.01
assert abs(r.simulation.potential.data.min()) < 0.01
finally:
inject.clear()
def test_init_from_config(self):
efconf = Config()
parser = ConfigParser()
parser.read_string(efconf.export_to_string())
sim = Config.from_configparser(parser).make()
assert sim.time_grid == TimeGrid(100, 1, 10)
assert sim.spat_mesh == SpatialMesh.do_init((10, 10, 10), (1, 1, 1), BoundaryConditionsConf(0))
assert sim.inner_regions == []
assert type(sim._field_solver) == FieldSolver
assert sim.particle_sources == []
assert sim.electric_fields == []
assert sim.magnetic_fields == []
assert sim.particle_interaction_model == ParticleInteractionModel("PIC")
assert sim._output_filename_prefix == "out_"
assert sim._output_filename_suffix == ".h5"
def test_cube_of_gas_with_hole(self, model, monkeypatch, tmpdir):
monkeypatch.chdir(tmpdir)
Config(TimeGridConf(1.0, save_step=.5, step=.1), SpatialMeshConf((10, 10, 10), (1, 1, 1)),
[ParticleSourceConf('gas', Box(size=(10, 10, 10)), 50, 0, np.zeros(3), 300)],
[InnerRegionConf('hole', Box(origin=(4, 4, 4), size=(2, 2, 2)))],
particle_interaction_model=ParticleInteractionModelConf(model)
).make().start_pic_simulation()
def test_id_generation(self, monkeypatch, tmpdir):
monkeypatch.chdir(tmpdir)
conf = Config(TimeGridConf(0.001, save_step=.0005, step=0.0001), SpatialMeshConf((10, 10, 10), (1, 1, 1)),
sources=[ParticleSourceConf('gas', Box((4, 4, 4), size=(1, 1, 1)), 50, 0, np.zeros(3), 0.00),
ParticleSourceConf('gas2', Box((5, 5, 5), size=(1, 1, 1)), 50, 0, np.zeros(3), 0.00)],
particle_interaction_model=ParticleInteractionModelConf('noninteracting')
)
assert len(conf.sources) == 2
sim = conf.make()
assert len(sim.particle_sources) == 2
assert len(sim.particle_arrays) == 0
sim.start_pic_simulation()
assert len(sim.particle_sources) == 2
assert len(sim.particle_arrays) == 2
assert_array_equal(sim.particle_arrays[0].ids, range(50))
assert_array_equal(sim.particle_arrays[1].ids, range(50, 100))
def test_conf_repr(self):
# noinspection PyUnresolvedReferences
from numpy import array # for use in eval
conf = Config(sources=[ParticleSourceConf()],
inner_regions=(InnerRegionConf(), ))
s = repr(conf)
c1 = eval(s)
assert_dataclass_eq(c1, conf)
def test_main(mocker, capsys, tmpdir, monkeypatch):
monkeypatch.chdir(tmpdir)
config = tmpdir.join("test_main.conf")
Config(time_grid=TimeGridConf(10, 5, 1)).export_to_fname("test_main.conf")
mocker.patch("sys.argv", ["main.py", str(config)])
main()
out, err = capsys.readouterr()
assert err == ""
assert out == f"""Config file is: {config}
def test_cube_of_gas(self, model, backend_and_solver):
sim = Config(TimeGridConf(1.0, save_step=.5, step=.1),
SpatialMeshConf((10, 10, 10), (1, 1, 1)), [
ParticleSourceConf('gas', Box(size=(10, 10, 10)), 50,
0, np.zeros(3), 300)
],
particle_interaction_model=ParticleInteractionModelConf(
model)).make()
Runner(sim).start()
def read_conf(parser, prefix, suffix, format_):
conf = Config.from_configparser(parser)
if prefix:
conf.output_file.prefix = prefix
if suffix:
conf.output_file.suffix = suffix
conf.output_file.format_ = format_
print(conf)
return conf
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 test_id_generation(self, backend_and_solver):
conf = Config(TimeGridConf(0.001, save_step=.0005, step=0.0001),
SpatialMeshConf((10, 10, 10), (1, 1, 1)),
sources=[
ParticleSourceConf('gas',
Box((4, 4, 4), size=(1, 1, 1)),
50, 0, np.zeros(3), 0.00),
ParticleSourceConf('gas2',
Box((5, 5, 5), size=(1, 1, 1)),
50, 0, np.zeros(3), 0.00)
],
particle_interaction_model=ParticleInteractionModelConf(
'noninteracting'))
assert len(conf.sources) == 2
sim = conf.make()
assert len(sim.particle_sources) == 2
assert len(sim.particle_arrays) == 0
Runner(sim).start()
assert len(sim.particle_sources) == 2
assert len(sim.particle_arrays) == 1
sim.particle_arrays[0].xp.testing.assert_array_equal(
sim.particle_arrays[0].ids, range(100))
def test_numbered(self, capsys, mocker):
mocker.patch('h5py.File')
sim = Config().make()
writer = OutputWriterNumberedH5('a_', '.b')
mocker.patch.object(writer, 'do_write')
assert writer.format_filename('test') == 'a_test.b'
assert writer.get_filename(sim) == '0000000'
writer.write(sim)
h5py.File.assert_called_once_with('a_0000000.b', 'w')
writer.do_write.assert_called_once()
out, err = capsys.readouterr()
assert err == ""
assert out == "Writing to file a_0000000.b\n"
def test_guess(tmpdir):
h5 = tmpdir.join("test.h5")
h5py.File(h5, 'w')
assert guess_input_type(h5) == (False, h5)
conf = tmpdir.join("test.conf")
Config().export_to_fname(conf)
p = ConfigParser()
p.read_string(Config().export_to_string())
assert guess_input_type(conf) == (True, p)
with raises(ArgumentTypeError):
guess_input_type(tmpdir.join('missing.txt'))
text = tmpdir.join('some.txt')
text.write('eowjfm ievmiefraivuenwaeofiunapewovjfiajief asdwouhd \n adfaef afef')
with raises(ArgumentTypeError):
guess_input_type(text)
data = tmpdir.join('some.bin')
data.write(bytes(range(255)), 'wb')
with raises(ArgumentTypeError):
guess_input_type(data)
def test_main(mocker, capsys, tmpdir, monkeypatch, solver_, backend_):
inject.clear()
monkeypatch.chdir(tmpdir)
config = tmpdir.join("test_main.conf")
Config(time_grid=TimeGridConf(10, 5, 1)).export_to_fname("test_main.conf")
argv = ["main.py", str(config)]
if solver_ != ' ':
argv += ["--solver", solver_]
if backend_ != ' ':
argv += ["--backend", backend_]
mocker.patch("sys.argv", argv)
main()
inject.clear()
out, err = capsys.readouterr()
assert err == ""
assert out == f"""Trying to guess input file type: {config}
### Config:
time_grid = TimeGridConf(total=10.0, save_step=5.0, step=1.0)
spatial_mesh = SpatialMeshConf(size=array([10., 10., 10.]), step=array([1., 1., 1.]))
sources = []
inner_regions = []
output_file = OutputFileConf(prefix='out_', suffix='.h5', format_='cpp')
boundary_conditions = BoundaryConditionsConf(right=0.0, left=0.0, bottom=0.0, top=0.0, near=0.0, far=0.0)
particle_interaction_model = ParticleInteractionModelConf(model='PIC')
external_fields = []
Writing initial fields to file
Writing to file out_fieldsWithoutParticles.h5
Writing step 0 to file
Writing to file out_0000000.h5
\rTime step from 0 to 1 of 10\rTime step from 1 to 2 of 10\rTime step from 2 to 3 of 10\rTime step from 3 to 4 of 10\rTime step from 4 to 5 of 10
Writing step 5 to file
Writing to file out_0000005.h5
\rTime step from 5 to 6 of 10\rTime step from 6 to 7 of 10\rTime step from 7 to 8 of 10\rTime step from 8 to 9 of 10\rTime step from 9 to 10 of 10
Writing step 10 to file
Writing to file out_0000010.h5
"""
argv = ["main.py", "out_0000005.h5"]
if solver_ != ' ':
argv += ["--solver", solver_]
if backend_ != ' ':
argv += ["--backend", backend_]
mocker.patch("sys.argv", argv)
main()
inject.clear()
out, err = capsys.readouterr()
assert err == ""
assert out == f"""Trying to guess input file type: out_0000005.h5
def construct_domain(config_or_h5_file):
extension = config_or_h5_file[config_or_h5_file.rfind(".") + 1:]
if extension == "h5":
with h5py.File(config_or_h5_file, 'r') as h5file:
filename_prefix, filename_suffix = \
extract_filename_prefix_and_suffix_from_h5filename(config_or_h5_file)
dom = Simulation.init_from_h5(h5file, filename_prefix,
filename_suffix)
continue_from_h5 = True
else:
conf = configparser.ConfigParser()
conf.read(config_or_h5_file)
echo_config(config_or_h5_file, conf)
dom = Config.from_configparser(conf).make()
continue_from_h5 = False
return dom, continue_from_h5
def test_read_conf():
p = ConfigParser()
c = Config(output_file=OutputFileConf("conf-prefix", "conf-suffix"))
p.read_string(c.export_to_string())
assert_dataclass_eq(read_conf(p, None, None, 'cpp'), c)
assert_dataclass_eq(read_conf(p, 'prefix2', None, 'cpp'),
Config(output_file=OutputFileConf("prefix2", "conf-suffix")))
assert_dataclass_eq(read_conf(p, 'prefix3', 'suffix3', 'cpp'),
Config(output_file=OutputFileConf("prefix3", "suffix3")))
assert_dataclass_eq(read_conf(p, None, 'suffix4', 'cpp'),
Config(output_file=OutputFileConf("conf-prefix", "suffix4")))
def test_is_trivial(backend):
assert BoundaryConditionsConf().is_the_same_on_all_boundaries
assert BoundaryConditionsConf(3.14).is_the_same_on_all_boundaries
assert not BoundaryConditionsConf(*range(6)).is_the_same_on_all_boundaries
assert not BoundaryConditionsConf(-1, 1, 1, 1, 1,
1).is_the_same_on_all_boundaries
assert Config().is_trivial()
assert Config(boundary_conditions=BoundaryConditionsConf(1)).is_trivial()
assert not Config(boundary_conditions=BoundaryConditionsConf(
1, 1, 1, 2, 1, 1)).is_trivial()
assert Config(
inner_regions=[InnerRegionConf(), InnerRegionConf()]).is_trivial()
assert Config(inner_regions=[
InnerRegionConf(potential=-2),
InnerRegionConf(potential=-2)
],
boundary_conditions=BoundaryConditionsConf(-2)).is_trivial()
assert not Config(inner_regions=[InnerRegionConf(
potential=1)]).is_trivial()
assert not Config(inner_regions=[
InnerRegionConf(potential=1),
InnerRegionConf(potential=0)
]).is_trivial()
def test_guess_stdin(tmpdir, monkeypatch):
monkeypatch.setattr('sys.stdin', StringIO(Config().export_to_string()))
p = ConfigParser()
p.read_string(Config().export_to_string())
assert guess_input_type('-') == (True, p)
def test_potentials():
assert Config().get_potentials() == [0., 0., 0., 0., 0., 0.]
def test_conf_export(self):
conf = Config(sources=[ParticleSourceConf()],
inner_regions=(InnerRegionConf(), ))
s = conf.export_to_string()
c1 = Config.from_string(s)
assert_dataclass_eq(c1, conf)
def test_example_conf(fname, tmpdir, monkeypatch, backend_and_solver):
sim = Config.from_fname(fname).make()
monkeypatch.chdir(tmpdir)
Runner(sim).start()
