def __init__(self):
self.datasets = {}
self.time = 0.
self.CM = DataContainer()
self.SP = DataContainer()
self.BC = DataContainer()
self.CM[CUBA.TIME_STEP] = 1.
self.CM[CUBA.NUMBER_OF_TIME_STEPS] = 10
# add lattice with temperature, mass and velocity data
lattice = make_tetragonal_lattice("lattice", 1., 1.1, (4, 5, 6))
size = numpy.prod(lattice.size)
new_node = []
for node in lattice.iter(item_type=CUBA.NODE):
index = numpy.prod(numpy.array(node.index)) + 1.0
node.data[CUBA.TEMPERATURE] = numpy.sin(index/size/2.)*size
node.data[CUBA.MASS] = index
new_node.append(node)
lattice.update(new_node)
self.datasets["lattice"] = lattice
# add particles from lattice
particles = Particles("particles")
for node in lattice.iter(item_type=CUBA.NODE):
particle = Particle(coordinates=node.index, data=node.data)
particle.data[CUBA.VELOCITY] = numpy.random.uniform(-0.1, 0.1, 3)
particles.add([particle])
self.datasets["particles"] = particles
# add mesh
mesh = Mesh("mesh")
points = numpy.array([
[0, 0, 0], [1, 0, 0], [0, 1, 0], [0, 0, 1],
[2, 0, 0], [3, 0, 0], [3, 1, 0], [2, 1, 0],
[2, 0, 1], [3, 0, 1], [3, 1, 1], [2, 1, 1]], 'f')
faces = [[2, 7, 11]]
# add points
point_iter = (Point(coordinates=point,
data=DataContainer(TEMPERATURE=index))
for index, point in enumerate(points))
uids = mesh.add(point_iter)
face_iter = (Face(points=[uids[index] for index in element],
data=DataContainer(TEMPERATURE=index,
VELOCITY=(index, 0., 0.)))
for index, element in enumerate(faces))
mesh.add(face_iter)
self.datasets["mesh"] = mesh
def create_example_particles():
points = array([[0, 0, 0], [1, 0, 0], [0, 1, 0], [0, 0, 1]], "f")
bonds = array([[0, 1], [0, 3], [1, 3, 2]])
temperature = array([10.0, 20.0, 30.0, 40.0])
particles = Particles("test")
uids = particles.add_particles(
Particle(coordinates=point, data=DataContainer(TEMPERATURE=temperature[index]))
for index, point in enumerate(points)
)
particles.add_bonds(
Bond(particles=[uids[index] for index in indices], data=DataContainer(TEMPERATURE=temperature[index]))
for indices in bonds
)
return particles
def test_closed_file_not_usable(self):
filename = os.path.join(self.temp_dir, 'test.cuds')
with closing(H5CUDS.open(filename)) as handle:
handle.add_dataset(Mesh(name="test_1"))
handle.add_dataset(Particles(name="test_2"))
lattice = make_cubic_lattice("test_3", 1.0, (2, 3, 4))
handle.add_dataset(lattice)
test_h1 = handle.get_dataset("test_1")
test_h2 = handle.get_dataset("test_2")
test_h3 = handle.get_dataset("test_3")
with self.assertRaises(Exception):
handle.get_dataset('test_h1')
with self.assertRaises(Exception):
test_h1.name = 'foo'
with self.assertRaises(Exception):
test_h2.name = 'foo'
with self.assertRaises(Exception):
test_h3.name = 'foo'
def test_with_cuds_particles(self):
# given
points = [
[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]
bonds = [[0, 1], [0, 3], [1, 3, 2]]
point_temperature = [10., 20., 30., 40.]
bond_temperature = [60., 80., 190.]
cuds = Particles('test')
particle_uids = cuds.add(
Particle(
coordinates=point,
data=DataContainer(
TEMPERATURE=point_temperature[index],
MASS=index))
for index, point in enumerate(points))
cuds.add(
Bond(
particles=[particle_uids[uid] for uid in indices],
data=DataContainer(
TEMPERATURE=bond_temperature[index],
MASS=index))
for index, indices in enumerate(bonds))
# when
data_set = cuds2vtk(cuds)
# then check points
self.assertEqual(data_set.GetNumberOfPoints(), 4)
coordinates = [
particle.coordinates for particle in cuds.iter(
item_type=CUBA.PARTICLE)]
vtk_points = [
data_set.GetPoint(index)
for index in range(len(particle_uids))]
self.assertItemsEqual(vtk_points, coordinates)
point_data = data_set.GetPointData()
self.assertEqual(point_data.GetNumberOfArrays(), 2)
arrays = {
point_data.GetArray(index).GetName(): point_data.GetArray(index)
for index in range(2)}
self.assertItemsEqual(arrays.keys(), ['MASS', 'TEMPERATURE'])
mass = vtk_to_numpy(arrays['MASS'])
self.assertItemsEqual(mass, range(4))
assert_array_equal(
vtk_to_numpy(arrays['TEMPERATURE']),
[point_temperature[int(index)] for index in mass])
# then check bonds
self.assertEqual(data_set.GetNumberOfCells(), 3)
links = [[
particle.coordinates
for particle in cuds.iter(bond.particles)]
for bond in cuds.iter(item_type=CUBA.BOND)]
vtk_lines = data_set.GetLines()
lines = [[
data_set.GetPoint(index) for index in line]
for line in iter_cells(vtk_lines)]
self.assertItemsEqual(lines, links)
cell_data = data_set.GetCellData()
self.assertEqual(cell_data.GetNumberOfArrays(), 2)
arrays = {
cell_data.GetArray(index).GetName(): cell_data.GetArray(index)
for index in range(2)}
self.assertItemsEqual(arrays.keys(), ['MASS', 'TEMPERATURE'])
mass = vtk_to_numpy(arrays['MASS'])
self.assertItemsEqual(mass, range(3))
assert_array_equal(
vtk_to_numpy(arrays['TEMPERATURE']),
[bond_temperature[int(index)] for index in mass])
from numpy import array
from simphony.cuds import Particles, Particle, Bond
from simphony.core.data_container import DataContainer
from simphony.core.cuba import CUBA
points = array([[0, 0, 0], [1, 0, 0], [0, 1, 0], [0, 0, 1]], 'f')
bonds = array([[0, 1], [0, 3], [1, 3, 2]])
temperature = array([10., 20., 30., 40.])
particles = Particles('test')
uids = particles.add_particles(
Particle(
coordinates=point,
data=DataContainer(TEMPERATURE=temperature[index]))
for index, point in enumerate(points))
particles.add_bonds(
Bond(particles=[uids[index] for index in indices])
for indices in bonds)
if __name__ == '__main__':
from simphony.visualisation import paraview_tools
# Visualise the Particles object
paraview_tools.show(particles, select=(CUBA.TEMPERATURE, 'particles'))
