def test_analog_multiple_hex():
"""This test tests that particle are sampled uniformly from a uniform source
defined on eight mesh volume elements in two energy groups. This is done
using the exact same method ass test_analog_multiple_hex.
"""
seed(1953)
m = Mesh(structured=True, structured_coords=[[0, 0.5, 1], [0, 0.5, 1], [0, 0.5, 1]], mats=None)
m.src = IMeshTag(2, float)
m.src[:] = np.ones(shape=(8, 2))
m.mesh.save("sampling_mesh.h5m")
sampler = Sampler("sampling_mesh.h5m", "src", np.array([0, 0.5, 1]), False)
num_samples = 5000
score = 1.0 / num_samples
num_divs = 2
tally = np.zeros(shape=(num_divs, num_divs, num_divs, num_divs))
for i in range(num_samples):
s = sampler.particle_birth([uniform(0, 1) for x in range(6)])
assert_equal(s[4], 1.0)
tally[int(s[0] * num_divs), int(s[1] * num_divs), int(s[2] * num_divs), int(s[3] * num_divs)] += score
for i in range(0, 4):
for j in range(0, 2):
halfspace_sum = np.sum(np.rollaxis(tally, i)[j, :, :, :])
assert abs(halfspace_sum - 0.5) / 0.5 < 0.1
def test_vtx_iterator():
#use vanilla izip as we"ll test using non-equal-length iterators
izip = itertools.izip
sm = Mesh(structured=True,
structured_coords =[range(10,15), range(21,25), range(31,34)])
it = sm.structured_set.iterate(iBase.Type.vertex, iMesh.Topology.point)
# test the default order
for (it_x, sm_x) in itertools.izip_longest(it,
sm.structured_iterate_vertex("zyx")):
assert_equal(it_x,sm_x)
# Do the same again, but use an arbitrary kwarg to structured_iterate_vertex
# to prevent optimization from kicking in
it.reset()
for (it_x, sm_x) in itertools.izip_longest(it,
sm.structured_iterate_vertex("zyx", no_opt=True)):
assert_equal(it_x,sm_x)
it.reset()
for (it_x, sm_x) in izip(it,
sm.structured_iterate_vertex("yx",z=sm.dims[2])):
assert_equal(it_x,sm_x)
it.reset()
for (it_x, sm_x) in izip(it, sm.structured_iterate_vertex("x")):
assert_equal(it_x,sm_x)
def test_analog_single_tet():
"""This test tests uniform sampling within a single tetrahedron. This is
done by dividing the tetrahedron in 4 smaller tetrahedrons and ensuring
that each sub-tet is sampled equally.
"""
seed(1953)
mesh = iMesh.Mesh()
v1 = [0, 0, 0]
v2 = [1, 0, 0]
v3 = [0, 1, 0]
v4 = [0, 0, 1]
verts = mesh.createVtx([v1, v2, v3, v4])
mesh.createEnt(iMesh.Topology.tetrahedron, verts)
m = Mesh(structured=False, mesh=mesh)
m.src = IMeshTag(1, float)
m.src[:] = np.array([1])
m.mesh.save("tet.h5m")
center = m.ve_center(list(m.iter_ve())[0])
subtets = [[center, v1, v2, v3], [center, v1, v2, v4], [center, v1, v3, v4], [center, v2, v3, v4]]
sampler = Sampler("tet.h5m", "src", np.array([0, 1]), False)
num_samples = 5000
score = 1.0 / num_samples
tally = np.zeros(shape=(4))
for i in range(num_samples):
s = sampler.particle_birth([uniform(0, 1) for x in range(6)])
assert_equal(s[4], 1.0)
for i, tet in enumerate(subtets):
if point_in_tet(tet, [s[0], s[1], s[2]]):
tally[i] += score
break
for t in tally:
assert abs(t - 0.25) / 0.25 < 0.2
def test_photon_source_hdf5_to_mesh():
"""Tests the function photon source_h5_to_mesh."""
if not HAVE_PYTAPS:
raise SkipTest
filename = os.path.join(thisdir, "files_test_alara", "phtn_src")
photon_source_to_hdf5(filename, chunkshape=(10,))
assert_true(os.path.exists(filename + ".h5"))
mesh = Mesh(structured=True, structured_coords=[[0, 1, 2], [0, 1, 2], [0, 1]])
tags = {("1001", "shutdown"): "tag1", ("TOTAL", "1 h"): "tag2"}
photon_source_hdf5_to_mesh(mesh, filename + ".h5", tags)
# create lists of lists of expected results
tag1_answers = [[1] + [0] * 41, [2] + [0] * 41, [3] + [0] * 41, [4] + [0] * 41]
tag2_answers = [[5] + [0] * 41, [6] + [0] * 41, [7] + [0] * 41, [8] + [0] * 41]
ves = list(mesh.structured_iterate_hex("xyz"))
for i, ve in enumerate(ves):
assert_array_equal(mesh.mesh.getTagHandle("tag1")[ve], tag1_answers[i])
assert_array_equal(mesh.mesh.getTagHandle("tag2")[ve], tag2_answers[i])
if os.path.isfile(filename + ".h5"):
os.remove(filename + ".h5")
def test_write_fluxin_single():
"""This function tests the flux_mesh_to_fluxin function for a single energy
group case.
"""
if not HAVE_PYTAPS:
raise SkipTest
output_name = "fluxin.out"
forward_fluxin = os.path.join(thisdir, "files_test_alara", "fluxin_single_forward.txt")
output = os.path.join(os.getcwd(), output_name)
flux_mesh = Mesh(structured=True, structured_coords=[[0, 1, 2], [0, 1, 2], [0, 1]])
tag_flux = flux_mesh.mesh.createTag("flux", 1, float)
flux_data = [1, 2, 3, 4]
ves = flux_mesh.structured_iterate_hex("xyz")
for i, ve in enumerate(ves):
tag_flux[ve] = flux_data[i]
# test forward writting
mesh_to_fluxin(flux_mesh, "flux", output_name, False)
with open(output) as f:
written = f.readlines()
with open(forward_fluxin) as f:
expected = f.readlines()
assert_equal(written, expected)
if os.path.isfile(output):
os.remove(output)
def test_analog_single_hex():
"""This test tests that particles of sampled evenly within the phase-space
of a single mesh volume element with one energy group in an analog sampling
scheme. This done by dividing each dimension (x, y, z, E) in half, then
sampling particles and tallying on the basis of which of the 2^4 = 8 regions
of phase space the particle is born into.
"""
seed(1953)
m = Mesh(structured=True, structured_coords=[[0, 1], [0, 1], [0, 1]], mats=None)
m.src = IMeshTag(1, float)
m.src[0] = 1.0
m.mesh.save("sampling_mesh.h5m")
sampler = Sampler("sampling_mesh.h5m", "src", np.array([0, 1]), False)
num_samples = 5000
score = 1.0 / num_samples
num_divs = 2
tally = np.zeros(shape=(num_divs, num_divs, num_divs, num_divs))
for i in range(num_samples):
s = sampler.particle_birth(np.array([uniform(0, 1) for x in range(6)]))
assert_equal(s[4], 1.0) # analog: all weights must be one
tally[int(s[0] * num_divs), int(s[1] * num_divs), int(s[2] * num_divs), int(s[3] * num_divs)] += score
# Test that each half-space of phase space (e.g. x > 0.5) is sampled about
# half the time.
for i in range(0, 4):
for j in range(0, 2):
assert abs(np.sum(np.rollaxis(tally, i)[j, :, :, :]) - 0.5) < 0.05
def gen_mesh(mats=()):
mesh_1 = Mesh(structured_coords=[[-1,0,1],[-1,0,1],[0,1]], structured=True,
structured_ordering='zyx', mats=mats)
volumes1 = list(mesh_1.structured_iterate_hex("xyz"))
flux_tag = mesh_1.mesh.createTag("flux", 1, float)
flux_data = [1.0, 2.0, 3.0, 4.0]
flux_tag[volumes1] = flux_data
return mesh_1
def test_get_divs():
x = [1, 2.5, 4, 6.9]
y = [-12, -10, -.5]
z = [100, 200]
sm = Mesh(structured_coords=[x, y, z], structured=True)
assert_equal(sm.structured_get_divisions("x"), x)
assert_equal(sm.structured_get_divisions("y"), y)
assert_equal(sm.structured_get_divisions("z"), z)
def test_iterate_3d():
# use izip_longest in the lockstep iterations below; this will catch any
# situations where one iterator turns out to be longer than expected.
sm = Mesh(structured=True,
structured_coords =[range(10,15), range(21,25), range(31,34)])
I = range(0,4)
J = range(0,3)
K = range(0,2)
izip = itertools.izip_longest
it = sm.structured_set.iterate(iBase.Type.region,
iMesh.Topology.hexahedron)
# Test the zyx order, which is default; it should be equivalent
# to the standard imesh iterator
for it_x, sm_x in izip(it, sm.structured_iterate_hex()):
assert_equal(it_x, sm_x)
#testing xyz
all_indices_zyx = itertools.product(I, J, K)
# Test the xyz order, the default from original mmGridGen
for ijk_index, sm_x in izip(all_indices_zyx,
sm.structured_iterate_hex("xyz")):
assert_equal(sm.structured_get_hex(*ijk_index), sm_x )
def _tuple_sort(collection, indices ):
# sorting function for order test
def t(tup):
# sort this 3-tuple according to the order of x, y, and z in
#indices
return (tup["xyz".find(indices[0])]*100 +
tup["xyz".find(indices[1])]*10 +
tup["xyz".find(indices[2])])
return sorted(collection, key = t)
def test_order(order, *args, **kw):
all_indices = itertools.product(*args)
for ijk_index, sm_x in izip(_tuple_sort(all_indices, order),
sm.structured_iterate_hex(order,**kw)):
assert_equal(sm.structured_get_hex(*ijk_index), sm_x)
test_order("yxz", I, J, K)
test_order("yzx", I, J, K)
test_order("xzy", I, J, K)
test_order("zxy", I, J, K)
# Specify z=[1] to iterator
test_order("xyz", I, J, [1], z=[1])
# Specify y=2 to iterator
test_order("zyx", I, [2], K, y=2)
# specify x and y both to iterator
test_order("yzx", [1,2,3],J[:-1], K, y=J[:-1], x=[1,2,3])
def test_bias_spatial():
"""This test tests a user-specified biasing scheme for which the only 1
bias group is supplied for a source distribution containing two energy
groups. This bias group is applied to both energy groups. In this test,
the user-supplied bias distribution that was choosen, correspondes to
uniform sampling, so that results can be checked against Case 1 in the
theory manual.
"""
seed(1953)
m = Mesh(structured=True, structured_coords=[[0, 3, 3.5], [0, 1], [0, 1]], mats=None)
m.src = IMeshTag(2, float)
m.src[:] = [[2.0, 1.0], [9.0, 3.0]]
m.bias = IMeshTag(1, float)
m.bias[:] = [1, 1]
e_bounds = np.array([0, 0.5, 1.0])
m.mesh.save("sampling_mesh.h5m")
sampler = Sampler("sampling_mesh.h5m", "src", e_bounds, "bias")
num_samples = 10000
score = 1.0 / num_samples
num_divs = 2
num_e = 2
spatial_tally = np.zeros(shape=(num_divs, num_divs, num_divs))
e_tally = np.zeros(shape=(4)) # number of phase space groups
for i in range(num_samples):
s = sampler.particle_birth(np.array([uniform(0, 1) for x in range(6)]))
if s[0] < 3.0:
assert_almost_equal(s[4], 0.7) # hand calcs
else:
assert_almost_equal(s[4], 2.8) # hand calcs
spatial_tally[int(s[0] * num_divs / 3.5), int(s[1] * num_divs / 1.0), int(s[2] * num_divs / 1.0)] += score
if s[0] < 3 and s[3] < 0.5:
e_tally[0] += score
elif s[0] < 3 and s[3] > 0.5:
e_tally[1] += score
if s[0] > 3 and s[3] < 0.5:
e_tally[2] += score
if s[0] > 3 and s[3] > 0.5:
e_tally[3] += score
for i in range(0, 3):
for j in range(0, 2):
halfspace_sum = np.sum(np.rollaxis(spatial_tally, i)[j, :, :])
assert abs(halfspace_sum - 0.5) / 0.5 < 0.1
expected_e_tally = [4.0 / 7, 2.0 / 7, 3.0 / 28, 1.0 / 28] # hand calcs
for i in range(4):
assert abs(e_tally[i] - expected_e_tally[i]) / expected_e_tally[i] < 0.1
def arithmetic_mesh_setup(self):
self.mesh_1 = Mesh(structured_coords=[[-1,0,1],[-1,0,1],[0,1]], structured=True)
volumes1 = list(self.mesh_1.structured_iterate_hex("xyz"))
volumes2 = list(self.mesh_1.structured_iterate_hex("xyz"))
flux_tag = self.mesh_1.mesh.createTag("flux", 1, float)
flux_data = [1.0, 2.0, 3.0, 4.0]
flux_tag[volumes1] = flux_data
self.mesh_2 = Mesh(structured_coords=[[-1,0,1],[-1,0,1],[0,1]], structured=True)
volumes1 = list(self.mesh_2.structured_iterate_hex("xyz"))
volumes2 = list(self.mesh_2.structured_iterate_hex("xyz"))
flux_tag = self.mesh_2.mesh.createTag("flux", 1, float)
flux_data = [1.1, 2.2, 3.3, 4.4]
flux_tag[volumes1] = flux_data
def test_structured_get_hex():
# mesh with valid i values 0-4, j values 0-3, k values 0-2
sm = Mesh(structured_coords = [range(11,16), range(21,25), range(31,34)],
structured=True)
def check(e):
assert_true(isinstance(e, iBase.Entity))
check(sm.structured_get_hex(0, 0, 0))
check(sm.structured_get_hex(1, 1, 1))
check(sm.structured_get_hex(3, 0, 0))
check(sm.structured_get_hex(3, 2, 1))
assert_raises(MeshError, sm.structured_get_hex,-1,-1,-1)
assert_raises(MeshError, sm.structured_get_hex, 4, 0, 0)
assert_raises(MeshError, sm.structured_get_hex, 0, 3, 0)
assert_raises(MeshError, sm.structured_get_hex, 0, 0, 2)
def test_structured_get_vertex():
# mesh with valid i values 0-4, j values 0-3, k values 0-2
x_range = np.array(range(10,15),dtype=np.float64)
y_range = np.array(range(21,24),dtype=np.float64)
z_range = np.array(range(31,33),dtype=np.float64)
sm = Mesh(structured_coords=[x_range, y_range, z_range], structured=True)
for i,x in enumerate(x_range):
for j,y in enumerate(y_range):
for k,z in enumerate(z_range):
print("{0} {1} {2}".format(i, j, k))
vtx = sm.structured_get_vertex(i,j,k)
vcoord = sm.mesh.getVtxCoords(vtx)
assert_true(all(vcoord == [x,y,z]))
def test_uniform():
"""This test tests that the uniform biasing scheme:
1. Samples space uniformly. This is checked using the same method
described in test_analog_single_hex().
2. Adjusts weights accordingly. Sample calculations are provided in Case 1
in the Theory Manual.
"""
seed(1953)
m = Mesh(structured=True, structured_coords=[[0, 3, 3.5], [0, 1], [0, 1]], mats=None)
m.src = IMeshTag(2, float)
m.src[:] = [[2.0, 1.0], [9.0, 3.0]]
e_bounds = np.array([0, 0.5, 1.0])
m.mesh.save("sampling_mesh.h5m")
sampler = Sampler("sampling_mesh.h5m", "src", e_bounds, True)
num_samples = 10000
score = 1.0 / num_samples
num_divs = 2
num_e = 2
spatial_tally = np.zeros(shape=(num_divs, num_divs, num_divs))
e_tally = np.zeros(shape=(4)) # number of phase space groups
for i in range(num_samples):
s = sampler.particle_birth(np.array([uniform(0, 1) for x in range(6)]))
if s[0] < 3.0:
assert_almost_equal(s[4], 0.7) # hand calcs
else:
assert_almost_equal(s[4], 2.8) # hand calcs
spatial_tally[int(s[0] * num_divs / 3.5), int(s[1] * num_divs / 1.0), int(s[2] * num_divs / 1.0)] += score
if s[0] < 3 and s[3] < 0.5:
e_tally[0] += score
elif s[0] < 3 and s[3] > 0.5:
e_tally[1] += score
if s[0] > 3 and s[3] < 0.5:
e_tally[2] += score
if s[0] > 3 and s[3] > 0.5:
e_tally[3] += score
for i in range(0, 3):
for j in range(0, 2):
halfspace_sum = np.sum(np.rollaxis(spatial_tally, i)[j, :, :])
assert abs(halfspace_sum - 0.5) / 0.5 < 0.1
expected_e_tally = [4.0 / 7, 2.0 / 7, 3.0 / 28, 1.0 / 28] # hand calcs
for i in range(4):
assert abs(e_tally[i] - expected_e_tally[i]) / expected_e_tally[i] < 0.1
def test_photon_sampling_setup_structured():
phtn_src = os.path.join(thisdir, "files_test_r2s", "phtn_src")
coords = [[0, 1, 2], [0, 1, 2], [0, 1]]
m = Mesh(structured=True, structured_coords=coords)
tags = {(10010000, "1 h"): "tag1", ("TOTAL", "shutdown"): "tag2"}
photon_sampling_setup(m, phtn_src, tags)
exp_tag1 = [[1.1, 2.2], [3.3, 4.4], [5.5, 6.6], [7.7, 8.8]]
exp_tag2 = [[11.1, 12.2], [13.3, 14.4], [15.5, 16.6], [17.7, 18.8]]
m.tag1 = IMeshTag(2, float)
m.tag2 = IMeshTag(2, float)
for i, mat, ve in m:
assert_array_equal(m.tag1[i], exp_tag1[i])
assert_array_equal(m.tag2[i], exp_tag2[i])
def test_magic_single_e():
"""Test a single energy group MAGIC case"""
# create mesh
coords = [[0, 1, 2], [-1, 3, 4], [10, 12]]
flux_data = [1.2, 3.3, 1.6, 1.7]
flux_error = [0.11, 0.013, 0.14, 0.19]
tally = Mesh(structured=True, structured_coords=coords)
tally.particle = "neutron"
tally.e_bounds = [0.0, 1.0]
tally.n_flux = IMeshTag(1, float)
tally.n_flux[:] = flux_data
tally.n_rel_error = IMeshTag(1, float)
tally.n_rel_error[:] = flux_error
tolerance = 0.15
null_value = 0.001
magic(tally, "n_flux", "n_rel_error", tolerance=tolerance, null_value=null_value)
expected_ww = [0.181818182, 0.5, 0.2424242, 0.001]
assert_array_almost_equal(tally.ww_x[:], expected_ww[:])
def test_magic_multi_bins():
"""Test multiple energy bins MAGIC case"""
# create a basic meshtally
coords = [[0, 1, 2], [-1, 3, 4], [10, 12]]
flux_data = [[1.2, 3.3], [1.6, 1.7], [1.5, 1.4], [2.6, 1.0]]
flux_error = [[0.11, 0.013], [0.14, 0.19], [0.02, 0.16], [0.04, 0.09]]
tally = Mesh(structured=True, structured_coords=coords)
tally.particle = "neutron"
tally.e_bounds = [0.0, 0.5, 1.0]
tally.n_flux = IMeshTag(2, float)
tally.n_flux[:] = flux_data
tally.n_rel_error = IMeshTag(2, float)
tally.n_rel_error[:] = flux_error
tolerance = 0.15
null_value = 0.001
magic(tally, "n_flux", "n_rel_error", tolerance=tolerance, null_value=null_value)
expected_ww = [[0.2307692308, 0.5],
[0.3076923077, 0.001],
[0.2884615385, 0.001],
[0.5, 0.15151515]]
assert_array_almost_equal(tally.ww_x[:], expected_ww[:])
def test_iterate_1d():
sm = Mesh(structured=True,
structured_coords =[range(10,15), range(21,25), range(31,34)])
def test_equal(ijk_list, miter):
for ijk, i in itertools.izip_longest(ijk_list, miter):
assert_equal(sm.structured_get_hex(*ijk), i)
test_equal([[0,0,0],[0,0,1]],
sm.structured_iterate_hex("z"))
test_equal([[0,1,1],[0,2,1]],
sm.structured_iterate_hex("y", y=[1,2], z=1))
test_equal([[2,0,0],[2,1,0],[2,2,0]],
sm.structured_iterate_hex("y", x=2))
test_equal([[0,0,0],[1,0,0],[2,0,0]],
sm.structured_iterate_hex("x", x=[0,1,2]))
def discretize_geom_centers():
from pyne import dagmc
dagmc.load(path)
coords = [0, 1]
coords2 = [0, 2, 4]
mesh = Mesh(structured=True,
structured_coords=[coords2, coords, coords])
# explicitly set to unstructured to trigger the ve centers sampling
# method
mesh.structured = False
res = dagmc.discretize_geom(mesh)
assert_array_equal(res["idx"], [0, 1])
assert_array_equal(res["cell"], [2, 3])
assert_array_equal(res["vol_frac"], [1.0, 1.0])
assert_array_equal(res["rel_error"], [1.0, 1.0])
# ensure kwargs are not accepted for unstructured mesh
assert_raises(ValueError, dagmc.discretize_geom, mesh, num_rays=3, grid=True)
def test_create_by_file():
filename = os.path.join(os.path.dirname(__file__),
"files_mesh_test/grid543.h5m")
sm = Mesh(mesh=filename, structured=True)
assert_true(all(sm.dims == [1, 11, -5, 5, 14, -3]))
# This mesh is interesting because the i/j/k space is not numbered from
# zero. Check that divisions are correct
assert_equal(sm.structured_get_divisions("x"), range(1,6))
assert_equal(sm.structured_get_divisions("y"), [1.0, 5.0, 10.0, 15.0] )
assert_equal(sm.structured_get_divisions("z"), [-10.0, 2.0, 12.0] )
# loading a test file without structured mesh metadata should raise an
# error
filename2 = os.path.join(os.path.dirname(__file__),
"files_mesh_test/no_str_mesh.h5m")
assert_raises(iBase.TagNotFoundError, Mesh, mesh=filename2,
structured=True)
def test_imeshtag_expand():
m = Mesh(structured=True, structured_coords=[[-1, 0, 1],[0, 1],[0, 1]])
m.clam = IMeshTag(2, float)
m.clam[:] = [[1.1, 2.2], [3.3, 4.4]]
m.clam.expand()
m.clam_000 = IMeshTag(1, float)
assert_array_equal(m.clam_000[:], [1.1, 3.3])
m.clam_001 = IMeshTag(1, float)
assert_array_equal(m.clam_001[:], [2.2, 4.4])
# corner case: mesh with a single volume element
m = Mesh(structured=True, structured_coords=[[0, 1],[0, 1],[0, 1]])
m.clam = IMeshTag(2, float)
m.clam[:] = [[1.1, 2.2]]
m.clam.expand()
m.clam_000 = IMeshTag(1, float)
assert_array_equal(m.clam_000[:], 1.1)
m.clam_001 = IMeshTag(1, float)
assert_array_equal(m.clam_001[:], 2.2)
def test_cadis_multiple_e():
"""Test multiple energy group CADIS case"""
adj_flux_tag = "adj_flux"
q_tag = "q"
ww_tag = "ww"
q_bias_tag= "q_bias"
#create meshes
coords = [[0, 1, 2], [-1, 3, 4], [10, 12]]
adj_flux_mesh = Mesh(structured=True, structured_coords=coords)
q_mesh = Mesh(structured=True, structured_coords=coords)
ww_mesh = Mesh(structured=True, structured_coords=coords)
q_bias_mesh = Mesh(structured=True, structured_coords=coords)
#add tags to input meshes
adj_flux_mesh.adj_flux = IMeshTag(2, float)
q_mesh.q = IMeshTag(2, float)
#create data for input meshes
adj_flux_data = [[1.1, 1.2], [1.3, 1.4], [0.0, 1.6], [1.7, 1.9]]
q_data = [[2.9, 2.8], [2.6, 2.5], [2.4, 2.2], [2.9, 0.0]]
#data data to mesh
adj_flux_mesh.adj_flux[:] = adj_flux_data
q_mesh.q[:] = q_data
#run cadis
cadis(adj_flux_mesh, adj_flux_tag, q_mesh, q_tag,
ww_mesh, ww_tag, q_bias_mesh, q_bias_tag, beta=5)
#expected results
expected_q_bias = [[0.0306200806, 0.0322518718], [0.0324438472, 0.0335956998],
[0.0, 0.0337876752], [0.0473219428, 0.0]]
expected_ww = [[0.3208302538, 0.2940943993], [0.2714717532, 0.2520809137],
[0.0, 0.2205707995], [0.2075960465, 0.1857438311]]
ww_mesh.ww = IMeshTag(2, float)
q_bias_mesh.q_bias = IMeshTag(2, float)
assert_array_almost_equal(ww_mesh.ww[:], expected_ww[:])
assert_array_almost_equal(q_bias_mesh.q_bias[:], expected_q_bias[:])
def test_discretize_geom_centers(self):
"""Test that unstructured mesh is sampled by mesh ve centers.
"""
if not HAVE_IMESH:
raise SkipTest
coords = [0, 1]
coords2 = [0, 2, 4]
mesh = Mesh(structured=True,
structured_coords=[coords2, coords, coords])
# explicitly set to unstructured to trigger the ve centers sampling
# method
mesh.structured = False
res = dagmc.discretize_geom(mesh)
assert_array_equal(res["idx"], [0, 1])
assert_array_equal(res["cell"], [2, 3])
assert_array_equal(res["vol_frac"], [1.0, 1.0])
assert_array_equal(res["rel_error"], [1.0, 1.0])
# ensure kwargs are not accepted for unstructured mesh
assert_raises(ValueError, dagmc.discretize_geom, mesh, num_rays=3, grid=True)
def test_bias():
"""This test tests that a user-specified biasing scheme:
1. Samples space uniformly according to the scheme.
2. Adjusts weights accordingly. Sample calculations are provided in Case 2
in the Theory Manual.
"""
seed(1953)
m = Mesh(structured=True, structured_coords=[[0, 3, 3.5], [0, 1], [0, 1]], mats=None)
m.src = IMeshTag(2, float)
m.src[:] = [[2.0, 1.0], [9.0, 3.0]]
e_bounds = np.array([0, 0.5, 1.0])
m.bias = IMeshTag(2, float)
m.bias[:] = [[1.0, 2.0], [3.0, 3.0]]
m.mesh.save("sampling_mesh.h5m")
sampler = Sampler("sampling_mesh.h5m", "src", e_bounds, "bias")
num_samples = 10000
score = 1.0 / num_samples
num_divs = 2
tally = np.zeros(shape=(4))
for i in range(num_samples):
s = sampler.particle_birth(np.array([uniform(0, 1) for x in range(6)]))
if s[0] < 3:
if s[3] < 0.5:
assert_almost_equal(s[4], 1.6) # hand calcs
tally[0] += score
else:
assert_almost_equal(s[4], 0.4) # hand calcs
tally[1] += score
else:
if s[3] < 0.5:
assert_almost_equal(s[4], 2.4) # hand calcs
tally[2] += score
else:
assert_almost_equal(s[4], 0.8) # hand calcs
tally[3] += score
expected_tally = [0.25, 0.5, 0.125, 0.125] # hand calcs
for a, b in zip(tally, expected_tally):
assert abs(a - b) / b < 0.25
def test_iterate_2d():
sm = Mesh(structured=True,
structured_coords =[range(10,15), range(21,25), range(31,34)])
def test_order(iter1, iter2):
for i1, i2 in itertools.izip_longest(iter1, iter2):
assert_equal(i1, i2)
test_order(sm.structured_iterate_hex("yx"),
sm.structured_iterate_hex("zyx", z=[0]))
test_order(sm.structured_iterate_hex("yx",z=1),
sm.structured_iterate_hex("zyx",z=[1]))
test_order(sm.structured_iterate_hex("yx",z=1),
sm.structured_iterate_hex("yzx",z=[1]))
test_order(sm.structured_iterate_hex("zy",x=[3]),
sm.structured_iterate_hex("zxy",x=3))
# Cannot iterate over multiple z's without specifing z order
assert_raises(MeshError, sm.structured_iterate_hex, "yx", z=[0,1])
def test_cadis_single_e():
"""Test single energy group cadis case"""
adj_flux_tag = "adj_flux"
q_tag = "q"
ww_tag = "ww"
q_bias_tag= "q_bias"
#create meshes
coords = [[0, 1, 2], [-1, 3, 4], [10, 12]]
adj_flux_mesh = Mesh(structured=True, structured_coords=coords)
q_mesh = Mesh(structured=True, structured_coords=coords)
ww_mesh = Mesh(structured=True, structured_coords=coords)
q_bias_mesh = Mesh(structured=True, structured_coords=coords)
#add tags to meshes
adj_flux_mesh.adj_flux = IMeshTag(1, float)
q_mesh.q = IMeshTag(1, float)
#create data for input meshes
adj_flux_data = [1.1, 1.3, 1.5, 1.7]
q_data = [2.9, 2.6, 2.4, 2.2]
#data data to mesh
adj_flux_mesh.adj_flux[:] = adj_flux_data
q_mesh.q[:] = q_data
#run CADIS
cadis(adj_flux_mesh, adj_flux_tag, q_mesh, q_tag,
ww_mesh, ww_tag, q_bias_mesh, q_bias_tag, beta=5)
#checkout output meshes
expected_ww = [0.3995338, 0.33806706, 0.29299145, 0.258521908]
expected_q_bias = [0.04652859, 0.04929988, 0.052508751, 0.0545507858]
ww_mesh.ww = IMeshTag(1, float)
q_bias_mesh.q_bias = IMeshTag(1, float)
assert_array_almost_equal(ww_mesh.ww[:], expected_ww[:])
assert_array_almost_equal(q_bias_mesh.q_bias[:], expected_q_bias[:])
def test_elem_volume():
"""Test the get_elem_volume method"""
# Test tet elements recognition and calculation
filename = os.path.join(os.path.dirname(__file__),
"files_mesh_test/unstr.h5m")
tetmesh = Mesh(mesh=filename)
vols = list()
for __, __, ve in tetmesh:
vols.append(tetmesh.elem_volume(ve))
assert_almost_equal(np.min(vols), 0.13973, places=5)
assert_almost_equal(np.max(vols), 2.1783, places=4)
assert_almost_equal(np.mean(vols), 0.52702, places=5)
# Test hex elements recognition and calculation
filename = os.path.join(os.path.dirname(__file__),
"files_mesh_test/grid543.h5m")
mesh = Mesh(mesh=filename)
vols = list()
for __, __, ve in mesh:
vols.append(mesh.elem_volume(ve))
assert_almost_equal(np.mean(vols), 51.3333, places=4)
def test_structured_hex_volume():
sm = Mesh(structured_coords = [[0,1,3], [-3,-2,0], [12,13,15]],
structured=True)
assert_equal(sm.structured_hex_volume(0,0,0), 1)
assert_equal(sm.structured_hex_volume(1,0,0), 2)
assert_equal(sm.structured_hex_volume(0,1,0), 2)
assert_equal(sm.structured_hex_volume(1,1,0), 4)
assert_equal(sm.structured_hex_volume(1,1,1), 8)
ijk_all = itertools.product(*([[0,1]]*3))
for V, ijk in itertools.izip_longest(sm.structured_iterate_hex_volumes(),
ijk_all):
assert_equal(V, sm.structured_hex_volume(*ijk))
def test_magic_below_tolerance():
"""Test MAGIC case when all flux errors are below the default tolerance"""
# create mesh
coords = [[0, 1, 2], [-1, 3, 4], [10, 12]]
flux_data = [1.2, 3.3, 1.6, 1.7]
flux_error = [0.11, 0.013, 0.14, 0.19]
tally = Mesh(structured=True, structured_coords=coords)
tally.particle = "neutron"
tally.e_bounds = [0.0, 0.5, 1.0]
tally.n_total_flux = IMeshTag(1, float)
tally.n_total_flux[:] = flux_data
tally.n_rel_error = IMeshTag(1, float)
tally.n_rel_error[:] = flux_error
magic(tally, "n_total_flux", "n_rel_error")
expected_ww = [0.181818182, 0.5, 0.2424242, 0.2575757576]
assert_array_almost_equal(tally.ww_x[:], expected_ww[:])
def test_ve_center():
m = Mesh(structured=True, structured_coords=[[-1, 3, 5], [-1, 1], [-1, 1]])
exp_centers = [(1, 0, 0), (4, 0, 0)]
for i, mat, ve in m:
assert_equal(m.ve_center(ve), exp_centers[i])
def irradiation_setup_structured(flux_tag="n_flux",
meshtal_file="meshtal_2x2x1"):
meshtal = os.path.join(thisdir, "files_test_r2s", meshtal_file)
tally_num = 4
cell_mats = {
2:
Material({2004: 1.0}, density=1.0, metadata={'name': 'mat_11'}),
3:
Material({
3007: 0.4,
3006: 0.6
},
density=2.0,
metadata={'name': 'mat_12'})
}
alara_params = "Bogus line for testing\n"
geom = os.path.join(thisdir, "unitbox.h5m")
num_rays = 9
grid = True
fluxin = os.path.join(os.getcwd(), "alara_fluxin")
reverse = True
alara_inp = os.path.join(os.getcwd(), "alara_inp")
alara_matlib = os.path.join(os.getcwd(), "alara_matlib")
output_mesh = os.path.join(os.getcwd(), "r2s_step1.h5m")
output_material = True
cell_fracs = np.zeros(8,
dtype=[('idx', np.int64), ('cell', np.int64),
('vol_frac', np.float64),
('rel_error', np.float64)])
cell_fracs[:] = [(0, 2, 0.037037037037037035, 0.5443310539518174),
(0, 3, 0.9629629629629631, 0.010467904883688123),
(1, 2, 0.037037037037037035, 0.5443310539518174),
(1, 3, 0.9629629629629629, 0.010467904883688454),
(2, 2, 0.037037037037037035, 0.5443310539518174),
(2, 3, 0.9629629629629629, 0.010467904883688454),
(3, 2, 0.037037037037037035, 0.5443310539518174),
(3, 3, 0.9629629629629629, 0.010467904883688454)]
irradiation_setup(meshtal, cell_mats, cell_fracs, alara_params, tally_num,
num_rays, grid, flux_tag, fluxin, reverse, alara_inp,
alara_matlib, output_mesh, output_material)
# expected output files
exp_alara_inp = os.path.join(thisdir, "files_test_r2s", "exp_alara_inp")
exp_alara_matlib = os.path.join(thisdir, "files_test_r2s",
"exp_alara_matlib")
exp_fluxin = os.path.join(thisdir, "files_test_r2s", "exp_fluxin")
# test files
f1 = filecmp.cmp(alara_inp, exp_alara_inp)
f2 = filecmp.cmp(alara_matlib, exp_alara_matlib)
f3 = filecmp.cmp(fluxin, exp_fluxin)
m = Mesh(structured=True, mesh=output_mesh, mats=output_mesh)
out = [
m.n_flux[:].tolist(), m.n_flux_err[:].tolist(),
m.n_flux_total[:].tolist(), m.n_flux_err_total[:].tolist(),
[x.comp.items() for y, x, z in m], [x.density for y, x, z in m]
]
n_flux = out[0]
n_flux_err = out[1]
n_flux_total = out[2]
n_flux_err_total = out[3]
densities = out[5]
comps = np.zeros(shape=(len(out[4])), dtype=dict)
for i, comp in enumerate(out[4]):
comps[i] = {}
for nucid in comp:
comps[i][nucid[0]] = nucid[1]
# test r2s step 1 output mesh
fluxes = [[6.93088E-07, 1.04838E-06], [6.36368E-07, 9.78475E-07],
[5.16309E-07, 9.86586E-07], [6.36887E-07, 9.29879E-07]]
errs = [[9.67452E-02, 7.55950E-02], [9.88806E-02, 7.61482E-02],
[1.04090E-01, 7.69284E-02], [9.75826E-02, 7.54181E-02]]
tot_fluxes = [1.74147E-06, 1.61484E-06, 1.50290E-06, 1.56677E-06]
tot_errs = [6.01522E-02, 6.13336E-02, 6.19920E-02, 5.98742E-02]
i = 0
for nf, nfe, nft, nfte, comp, density in izip(n_flux, n_flux_err,
n_flux_total,
n_flux_err_total, comps,
densities):
assert_almost_equal(density, 1.962963E+00)
assert_equal(len(comp), 3)
assert_almost_equal(comp[20040000], 1.886792E-02)
assert_almost_equal(comp[30060000], 5.886792E-01)
assert_almost_equal(comp[30070000], 3.924528E-01)
assert_array_equal(nf, fluxes[i])
assert_array_equal(nfe, errs[i])
assert_almost_equal(nft, tot_fluxes[i])
assert_almost_equal(nfte, tot_errs[i])
i += 1
os.remove(alara_inp)
os.remove(alara_matlib)
os.remove(fluxin)
os.remove(output_mesh)
return [f1, f2, f3]
def test_mesh_to_geom():
if not HAVE_PYMOAB:
raise SkipTest
mats = {
0: Material({
'H1': 1.0,
'K39': 1.0
}, density=42.0),
1: Material({
'H1': 0.1,
'O16': 1.0
}, density=43.0),
2: Material({'He4': 42.0}, density=44.0),
3: Material({'Tm171': 171.0}, density=45.0),
4: Material({'C12': 1.0}, density=47.0),
5: Material({'1002': 1.0}, density=5.0),
}
m = Mesh(structured_coords=[[0, 1, 2, 3], [0, 1, 2], [0, 1]],
mats=mats,
structured=True)
geom = mcnp.mesh_to_geom(m)
exp_geom = ("Generated from PyNE Mesh\n"
"1 1 42.0 1 -2 5 -6 8 -9\n"
"2 2 43.0 1 -2 6 -7 8 -9\n"
"3 3 44.0 2 -3 5 -6 8 -9\n"
"4 4 45.0 2 -3 6 -7 8 -9\n"
"5 5 47.0 3 -4 5 -6 8 -9\n"
"6 6 5.0 3 -4 6 -7 8 -9\n"
"7 0 -1:4:-5:7:-8:9\n"
"\n"
"1 px 0.0\n"
"2 px 1.0\n"
"3 px 2.0\n"
"4 px 3.0\n"
"5 py 0.0\n"
"6 py 1.0\n"
"7 py 2.0\n"
"8 pz 0.0\n"
"9 pz 1.0\n"
"\n"
"C density = 42.0\n"
"m1\n"
" 1001 -5.0000e-01\n"
" 19039 -5.0000e-01\n"
"C density = 43.0\n"
"m2\n"
" 1001 -9.0909e-02\n"
" 8016 -9.0909e-01\n"
"C density = 44.0\n"
"m3\n"
" 2004 -1.0000e+00\n"
"C density = 45.0\n"
"m4\n"
" 69171 -1.0000e+00\n"
"C density = 47.0\n"
"m5\n"
" 6012 -1.0000e+00\n"
"C density = 5.0\n"
"m6\n"
" 1002 -1.0000e+00\n")
assert_equal(geom, exp_geom)
def test_structured_mesh_from_coords():
sm = Mesh(structured_coords = [range(1,5), range(1,4), range(1,3)], \
structured=True)
assert_true(all(sm.dims == [0, 0, 0, 3, 2, 1]))
def write_partisn_input_options():
if not HAVE_PYMOAB:
raise SkipTest
"""Test PARTISN input file creation with a slew of keyword arguments
"""
THIS_DIR = os.path.dirname(os.path.realpath(__file__))
hdf5 = os.path.join(THIS_DIR, "files_test_partisn",
"partisn_test_geom.h5m")
input_file = os.path.join(THIS_DIR, "files_test_partisn",
"partisn_options.inp")
file_expected = os.path.join(THIS_DIR, "files_test_partisn",
"partisn_options_expected.inp")
sc = [-5.0, 0.0, 10.0, 15.0], [-5.0, 5.0], [-5.0, 5.0]
mesh = Mesh(structured_coords=sc, structured=True)
ngroup = 66
dg = np.zeros(
4,
dtype=[
("idx", np.int64),
("cell", np.int64),
("vol_frac", np.float64),
("rel_error", np.float64),
],
)
dg[:] = [
(0, 1, 1.0, 0.0),
(1, 1, 0.5, 0.04714045207910317),
(1, 2, 0.5, 0.04714045207910317),
(2, 2, 1.0, 0.0),
]
mat_assigns = {
1: "mat:Helium, Natural",
2: "mat:Mercury",
5: "mat:Graveyard",
6: "mat:Vacuum",
}
cards = {
"block1": {
"isn": 6,
"maxlcm": 6000000,
"maxscm": 3000000,
},
"block2": {
"hello": "from block2"
},
"block3": {
"i2lp1": 0,
"ifido": 1,
"ihm": 227,
"ihs": 11,
"iht": 10,
"ititl": 1,
"kwikrd": 1,
"lib": "xsf21-71",
"lng": 175,
"maxord": 5,
"savbxs": 1,
},
"block4": {
"hello": "from block4"
},
"block5": {
"source": "<this is a dummy source>"
},
}
with warnings.catch_warnings(record=True) as w:
partisn.write_partisn_input(
mesh,
hdf5,
ngroup,
input_file=input_file,
dg=dg,
mat_assigns=mat_assigns,
fine_per_coarse=3,
cards=cards,
num_rays=9,
) # include num_rays to get warning
# verify we get a warning from including num_rays and dg
out1 = len(w) == 1
out2 = filecmp.cmp(input_file, file_expected)
os.remove(input_file)
return out1 and out2
def test_unstructured_mesh_from_instance():
filename = os.path.join(os.path.dirname(__file__),
"files_mesh_test/unstr.h5m")
mesh = mb_core.Core()
mesh.load_file(filename)
sm = Mesh(mesh=mesh)
def test_irradiation_setup_unstructured():
flux_tag = "n_flux"
meshtal_file = os.path.join(thisdir, "files_test_r2s", "meshtal_2x2x1")
meshtal = Meshtal(
meshtal_file, {
4: (flux_tag, flux_tag + "_err", flux_tag + "_total",
flux_tag + "_err_total")
})
# Explicitly make this mesh unstructured, it will now iterate in yxz
# order which is MOAB structured mesh creation order.
meshtal = Mesh(structured=False, mesh=meshtal.tally[4].mesh)
meshtal_mesh_file = os.path.join(thisdir, "meshtal.h5m")
meshtal.mesh.save(meshtal_mesh_file)
cell_mats = {
2: Material({2004: 1.0}, density=1.0),
3: Material({
3007: 0.4,
3006: 0.6
}, density=2.0)
}
alara_params = "Bogus line for testing"
geom = os.path.join(thisdir, "unitbox.h5m")
flux_tag = "n_flux"
fluxin = os.path.join(os.getcwd(), "alara_fluxin")
reverse = True
alara_inp = os.path.join(os.getcwd(), "alara_inp")
alara_matlib = os.path.join(os.getcwd(), "alara_matlib")
output_mesh = os.path.join(os.getcwd(), "r2s_step1.h5m")
irradiation_setup(flux_mesh=meshtal_mesh_file,
cell_mats=cell_mats,
alara_params=alara_params,
geom=geom,
flux_tag=flux_tag,
fluxin=fluxin,
reverse=reverse,
alara_inp=alara_inp,
alara_matlib=alara_matlib,
output_mesh=output_mesh)
# expected output files
exp_alara_inp = os.path.join(thisdir, "files_test_r2s", "exp_alara_inp")
exp_alara_matlib = os.path.join(thisdir, "files_test_r2s",
"exp_alara_matlib_un")
exp_fluxin = os.path.join(thisdir, "files_test_r2s", "exp_fluxin_un")
# test alara input file
with open(alara_inp, 'r') as f1, open(exp_alara_inp, 'r') as f2:
for a, b in zip(f1.readlines(), f2.readlines()):
assert_equal(a, b)
# test alara matlibe file
with open(alara_matlib, 'r') as f1, open(exp_alara_matlib) as f2:
for a, b in zip(f1.readlines(), f2.readlines()):
assert_equal(a, b)
# test alara fluxin file
with open(fluxin, 'r') as f1, open(exp_fluxin) as f2:
for a, b in zip(f1.readlines(), f2.readlines()):
assert_equal(a, b)
# test r2s step 1 output mesh
fluxes = [[6.93088E-07, 1.04838E-06], [6.36368E-07, 9.78475E-07],
[5.16309E-07, 9.86586E-07], [6.36887E-07, 9.29879E-07]]
errs = [[9.67452E-02, 7.55950E-02], [9.88806E-02, 7.61482E-02],
[1.04090E-01, 7.69284E-02], [9.75826E-02, 7.54181E-02]]
tot_fluxes = [1.74147E-06, 1.61484E-06, 1.50290E-06, 1.56677E-06]
tot_errs = [6.01522E-02, 6.13336E-02, 6.19920E-02, 5.98742E-02]
m = Mesh(structured=True, mesh=output_mesh, mats=output_mesh)
for i, mat, _ in m:
assert_almost_equal(mat.density, 2.0)
assert_equal(len(mat.comp), 2)
assert_almost_equal(mat.comp[30060000], 0.6)
assert_almost_equal(mat.comp[30070000], 0.4)
assert_array_equal(m.n_flux[i], fluxes[i])
assert_array_equal(m.n_flux_err[i], errs[i])
assert_almost_equal(m.n_flux_total[i], tot_fluxes[i])
assert_almost_equal(m.n_flux_err_total[i], tot_errs[i])
os.remove(meshtal_mesh_file)
os.remove(alara_inp)
os.remove(alara_matlib)
os.remove(fluxin)
os.remove(output_mesh)
import numpy as np
from pyne.cccc import Atflux
from pyne.mesh import Mesh, NativeMeshTag
sc = [
np.linspace(-600, 1200, 46),
np.linspace(-800, 500, 31),
np.linspace(-500, 500, 26)
]
m = Mesh(structured=True, structured_coords=sc, mats=None)
at = Atflux("atflux")
at.to_mesh(m, "flux")
m.flux = NativeMeshTag(217, float)
m.save("adj_p.h5m")
def get_zones_iteration_order():
"""Test that _get_zones function gives results in zyx order.
"""
try:
from pyne import dagmc
except:
raise SkipTest
if not HAVE_PYMOAB:
raise SkipTest
# hdf5 test file
THIS_DIR = os.path.dirname(os.path.realpath(__file__))
hdf5 = THIS_DIR + '/files_test_partisn/fractal_box.h5m'
data_hdf5path = '/materials'
nuc_hdf5path = '/nucid'
# Load dagmc geometry
dagmc.load(hdf5)
bounds = [-5., 0., 5.]
sc = [bounds] * 3
mesh = Mesh(structured_coords=sc, structured=True)
bounds = {'x': bounds, 'y': bounds, 'z': bounds}
num_rays = 9
grid = True
dg = None
mat_assigns = None
unique_names = {
'mat:m1': 'M1',
'mat:m2': 'M2',
'mat:m3': 'M3',
'mat:m4': 'M4'
}
voxel_zones, zones = partisn._get_zones(mesh, hdf5, bounds, num_rays, grid,
dg, mat_assigns, unique_names)
voxel_zones_expected = np.array([[1, 2], [1, 4], [1, 3], [1, 4]])
zones_expected = {
1: {
'vol_frac': [1.0],
'mat': ['M2']
},
2: {
'vol_frac': [1.0],
'mat': ['M4']
},
3: {
'vol_frac': [1.0],
'mat': ['M1']
},
4: {
'vol_frac': [1.0],
'mat': ['M3']
}
}
vz_tf = voxel_zones.all() == voxel_zones_expected.all()
z_tf = zones == zones_expected
return [vz_tf, z_tf]
def get_zones_with_void():
"""Test the _get_zones function if a void is present.
"""
try:
from pyne import dagmc
except:
raise SkipTest
if not HAVE_PYMOAB:
raise SkipTest
# hdf5 test file
THIS_DIR = os.path.dirname(os.path.realpath(__file__))
hdf5 = THIS_DIR + '/files_test_partisn/partisn_test_geom.h5m'
data_hdf5path = '/materials'
nuc_hdf5path = '/nucid'
dagmc.load(hdf5)
# mesh
xvals = [-5., 0., 10., 15., 15.1]
yvals = [-5., 0., 5.]
zvals = [-5., 0., 5.]
mesh = Mesh(structured_coords=[xvals, yvals, zvals],
structured=True,
structured_ordering='xyz')
# more inputs
bounds = {'x': xvals, 'y': yvals, 'z': zvals}
num_rays = 400
grid = True
dg = None
mat_assigns = None
unique_names = {
'mat:Helium, Natural': 'HELIUMNA',
'mat:Mercury': 'MERCURY1'
}
voxel_zones, zones = partisn._get_zones(mesh, hdf5, bounds, num_rays, grid,
dg, mat_assigns, unique_names)
# expected results
voxel_zones_expected = np.array([[1, 1, 1, 1], [2, 2, 2, 2], [3, 3, 3, 3],
[0, 0, 0, 0]])
zones_expected = {
1: {
'vol_frac': [1.0],
'mat': [u'HELIUMNA']
},
2: {
'vol_frac': [0.5, 0.5],
'mat': [u'HELIUMNA', u'MERCURY1']
},
3: {
'vol_frac': [1.0],
'mat': [u'MERCURY1']
}
}
vz_tf = False
z_tf = False
if voxel_zones.all() == voxel_zones_expected.all():
vz_tf = True
if zones == zones_expected:
z_tf = True
#assert(voxel_zones.all() == voxel_zones_expected.all())
#assert(zones == zones_expected)
return [vz_tf, z_tf]
def test_cadis_multiple_e():
"""Test multiple energy group CADIS case"""
adj_flux_tag = "adj_flux"
q_tag = "q"
ww_tag = "ww"
q_bias_tag = "q_bias"
# create meshes
coords = [[0, 1, 2], [-1, 3, 4], [10, 12]]
adj_flux_mesh = Mesh(structured=True, structured_coords=coords)
q_mesh = Mesh(structured=True, structured_coords=coords)
ww_mesh = Mesh(structured=True, structured_coords=coords)
q_bias_mesh = Mesh(structured=True, structured_coords=coords)
# add tags to input meshes
adj_flux_mesh.adj_flux = NativeMeshTag(2, float)
q_mesh.q = NativeMeshTag(2, float)
# create data for input meshes
adj_flux_data = [[1.1, 1.2], [1.3, 1.4], [0.0, 1.6], [1.7, 1.9]]
q_data = [[2.9, 2.8], [2.6, 2.5], [2.4, 2.2], [2.9, 0.0]]
# data data to mesh
adj_flux_mesh.adj_flux[:] = adj_flux_data
q_mesh.q[:] = q_data
# run cadis
cadis(
adj_flux_mesh,
adj_flux_tag,
q_mesh,
q_tag,
ww_mesh,
ww_tag,
q_bias_mesh,
q_bias_tag,
beta=5,
)
# expected results
expected_q_bias = [
[0.0306200806, 0.0322518718],
[0.0324438472, 0.0335956998],
[0.0, 0.0337876752],
[0.0473219428, 0.0],
]
expected_ww = [
[0.3208302538, 0.2940943993],
[0.2714717532, 0.2520809137],
[0.0, 0.2205707995],
[0.2075960465, 0.1857438311],
]
ww_mesh.ww = NativeMeshTag(2, float)
q_bias_mesh.q_bias = NativeMeshTag(2, float)
assert_array_almost_equal(ww_mesh.ww[:], expected_ww[:])
assert_array_almost_equal(q_bias_mesh.q_bias[:], expected_q_bias[:])
def test_cadis_single_e():
"""Test single energy group cadis case"""
adj_flux_tag = "adj_flux"
q_tag = "q"
ww_tag = "ww"
q_bias_tag = "q_bias"
# create meshes
coords = [[0, 1, 2], [-1, 3, 4], [10, 12]]
adj_flux_mesh = Mesh(structured=True, structured_coords=coords)
q_mesh = Mesh(structured=True, structured_coords=coords)
ww_mesh = Mesh(structured=True, structured_coords=coords)
q_bias_mesh = Mesh(structured=True, structured_coords=coords)
# add tags to meshes
adj_flux_mesh.adj_flux = NativeMeshTag(1, float)
q_mesh.q = NativeMeshTag(1, float)
# create data for input meshes
adj_flux_data = [1.1, 1.3, 1.5, 1.7]
q_data = [2.9, 2.6, 2.4, 2.2]
# data data to mesh
adj_flux_mesh.adj_flux[:] = adj_flux_data
q_mesh.q[:] = q_data
# run CADIS
cadis(
adj_flux_mesh,
adj_flux_tag,
q_mesh,
q_tag,
ww_mesh,
ww_tag,
q_bias_mesh,
q_bias_tag,
beta=5,
)
# checkout output meshes
expected_ww = [0.3995338, 0.33806706, 0.29299145, 0.258521908]
expected_q_bias = [0.04652859, 0.04929988, 0.052508751, 0.0545507858]
ww_mesh.ww = NativeMeshTag(1, float)
q_bias_mesh.q_bias = NativeMeshTag(1, float)
assert_array_almost_equal(ww_mesh.ww[:], expected_ww[:])
assert_array_almost_equal(q_bias_mesh.q_bias[:], expected_q_bias[:])
def main():
msg = ("This script reads a mesh (.h5m) file and, for each vector tag of\n"
"length N, creates N scalar tags. This is useful for visualizing\n"
"data on mesh with programs that do not support vector tags.\n")
parser = argparse.ArgumentParser(msg)
parser.add_argument("mesh_file", help="The path the mesh file")
parser.add_argument(
"-o",
dest="output",
default="expanded_tags.vtk",
help="The name of the output file",
)
parser.add_argument(
"-t",
"--tags",
dest="tags",
default=None,
help=("Instead of expanding all tags, only expand tags\n"
"within this list. Tag names listed here should\n"
"be seperated by commas without spaces.\n"),
)
args = parser.parse_args()
try:
from pymoab import types
except ImportError:
warn(
"The PyMOAB optional dependency could not be imported. "
"Some aspects of the mesh module may be incomplete.",
ImportWarning,
)
try:
m = Mesh(structured=True, mesh=args.mesh_file)
except types.MB_TAG_NOT_FOUND:
sys.stderr.write("Structured mesh not found\n \
trying unstructured mesh \n")
m = Mesh(structured=False, mesh=args.mesh_file)
if args.tags is not None:
tags = args.tags.split(",")
else:
tags = []
for name, tag in m.tags.items():
if isinstance(tag, NativeMeshTag) and name != "idx":
tags.append(name)
for tag in tags:
m.tag = NativeMeshTag(name=tag)
# there may be vector tags
try:
# this line fails if the tag is a scalar tag
m.tag.size = len(m.tag[0])
except TypeError:
sys.stderr.write("Vector tag not found, assuming scalar tag \n")
m.tag.size = 1
if m.tag.size > 1:
print("Expanding tag: {}".format(tag))
m.tag.expand()
print("Saving file {}".format(args.output))
m.write_hdf5(args.output)
print("Complete")
def test_nativetag_expand():
m = Mesh(structured=True, structured_coords=[[-1, 0, 1], [0, 1], [0, 1]])
m.clam = NativeMeshTag(2, float)
m.clam[:] = [[1.1, 2.2], [3.3, 4.4]]
m.clam.expand()
m.clam_000 = NativeMeshTag(1, float)
assert_array_equal(m.clam_000[:], [1.1, 3.3])
m.clam_001 = NativeMeshTag(1, float)
assert_array_equal(m.clam_001[:], [2.2, 4.4])
# corner case: mesh with a single volume element
m = Mesh(structured=True, structured_coords=[[0, 1], [0, 1], [0, 1]])
m.clam = NativeMeshTag(2, float)
m.clam[:] = [[1.1, 2.2]]
m.clam.expand()
m.clam_000 = NativeMeshTag(1, float)
assert_array_equal(m.clam_000[:], 1.1)
m.clam_001 = NativeMeshTag(1, float)
assert_array_equal(m.clam_001[:], 2.2)
def test_multiple_meshtally_meshtal():
"""Test a meshtal file containing 4 mesh tallies including neutron and
photon, single energy group and multiple energy group.
"""
if not HAVE_PYMOAB:
raise SkipTest
thisdir = os.path.dirname(__file__)
meshtal_file = os.path.join(thisdir, "mcnp_meshtal_multiple_meshtal.txt")
expected_h5m_4 = os.path.join(thisdir, "mcnp_meshtal_tally_4.h5m")
expected_sm_4 = Mesh(mesh=expected_h5m_4, structured=True)
expected_h5m_14 = os.path.join(thisdir, "mcnp_meshtal_tally_14.h5m")
expected_sm_14 = Mesh(mesh=expected_h5m_14, structured=True)
expected_h5m_24 = os.path.join(thisdir, "mcnp_meshtal_tally_24.h5m")
expected_sm_24 = Mesh(mesh=expected_h5m_24, structured=True)
expected_h5m_34 = os.path.join(thisdir, "mcnp_meshtal_tally_34.h5m")
expected_sm_34 = Mesh(mesh=expected_h5m_34, structured=True)
tags = {
4: ["n_result", "n_rel_error", "n_total_result", "n_total_rel_error"],
14: ["n_result", "n_rel_error", "n_total_result", "n_total_rel_error"],
24: ["p_result", "p_rel_error", "p_total_result", "p_total_rel_error"],
34: ["p_result", "p_rel_error", "p_total_result", "p_total_rel_error"]
}
meshtal_object = mcnp.Meshtal(meshtal_file, tags)
assert_equal(meshtal_object.version, '5')
assert_equal(meshtal_object.tally[4].mats, None)
# test meshtally 4
for v_e, expected_v_e in zip(
meshtal_object.tally[4].structured_iterate_hex("xyz"),
expected_sm_4.structured_iterate_hex("xyz")):
written = meshtal_object.tally[4].n_result[v_e]
expected = expected_sm_4.n_result[expected_v_e]
assert_array_equal(written, expected)
for v_e, expected_v_e in zip(
meshtal_object.tally[4].structured_iterate_hex("xyz"),
expected_sm_4.structured_iterate_hex("xyz")):
written = meshtal_object.tally[4].n_rel_error[v_e]
expected = expected_sm_4.n_rel_error[expected_v_e]
assert_array_equal(written, expected)
for v_e, expected_v_e in zip(
meshtal_object.tally[4].structured_iterate_hex("xyz"),
expected_sm_4.structured_iterate_hex("xyz")):
written = meshtal_object.tally[4].n_total_result[v_e]
expected = expected_sm_4.n_total_result[expected_v_e]
assert_equal(written, expected)
for v_e, expected_v_e in zip(
meshtal_object.tally[4].structured_iterate_hex("xyz"),
expected_sm_4.structured_iterate_hex("xyz")):
written = meshtal_object.tally[4].n_total_rel_error[v_e]
expected = expected_sm_4.n_total_rel_error[expected_v_e]
assert_equal(written, expected)
# test meshtally 14
for v_e, expected_v_e in zip(
meshtal_object.tally[14].structured_iterate_hex("xyz"),
expected_sm_14.structured_iterate_hex("xyz")):
written = meshtal_object.tally[14].n_result[v_e]
expected = expected_sm_14.n_result[expected_v_e]
assert_array_equal(written, expected)
for v_e, expected_v_e in zip(
meshtal_object.tally[14].structured_iterate_hex("xyz"),
expected_sm_14.structured_iterate_hex("xyz")):
written = meshtal_object.tally[14].n_rel_error[v_e]
expected = expected_sm_14.n_rel_error[expected_v_e]
assert_array_equal(written, expected)
# test meshtally 24
for v_e, expected_v_e in zip(
meshtal_object.tally[24].structured_iterate_hex("xyz"),
expected_sm_24.structured_iterate_hex("xyz")):
written = meshtal_object.tally[24].p_result[v_e]
expected = expected_sm_24.p_result[expected_v_e]
assert_array_equal(written, expected)
for v_e, expected_v_e in zip(
meshtal_object.tally[24].structured_iterate_hex("xyz"),
expected_sm_24.structured_iterate_hex("xyz")):
written = meshtal_object.tally[24].p_rel_error[v_e]
expected = expected_sm_24.p_rel_error[expected_v_e]
assert_array_equal(written, expected)
for v_e, expected_v_e in zip(
meshtal_object.tally[24].structured_iterate_hex("xyz"),
expected_sm_24.structured_iterate_hex("xyz")):
written = meshtal_object.tally[24].p_total_result[v_e]
expected = expected_sm_24.p_total_result[expected_v_e]
assert_equal(written, expected)
for v_e, expected_v_e in zip(
meshtal_object.tally[24].structured_iterate_hex("xyz"),
expected_sm_24.structured_iterate_hex("xyz")):
written = meshtal_object.tally[24].p_total_rel_error[v_e]
expected = expected_sm_24.p_total_rel_error[expected_v_e]
assert_equal(written, expected)
# test meshtally 34
for v_e, expected_v_e in zip(
meshtal_object.tally[34].structured_iterate_hex("xyz"),
expected_sm_34.structured_iterate_hex("xyz")):
written = meshtal_object.tally[34].p_result[v_e]
expected = expected_sm_34.p_result[expected_v_e]
assert_array_equal(written, expected)
for v_e, expected_v_e in zip(
meshtal_object.tally[34].structured_iterate_hex("xyz"),
expected_sm_34.structured_iterate_hex("xyz")):
written = meshtal_object.tally[34].p_rel_error[v_e]
expected = expected_sm_34.p_rel_error[expected_v_e]
assert_array_equal(written, expected)
def irradiation_setup_unstructured(flux_tag="n_flux"):
meshtal_filename = "meshtal_2x2x1"
meshtal_file = os.path.join(thisdir, "files_test_r2s", meshtal_filename)
meshtal = Meshtal(
meshtal_file, {
4: (flux_tag, flux_tag + "_err", flux_tag + "_total",
flux_tag + "_err_total")
})
# Explicitly make this mesh unstructured, it will now iterate in yxz
# order which is MOAB structured mesh creation order.
meshtal = Mesh(structured=False, mesh=meshtal.tally[4].mesh)
meshtal_mesh_file = os.path.join(thisdir, "meshtal.h5m")
meshtal.write_hdf5(meshtal_mesh_file, write_mats=False)
if flux_tag != "n_flux":
# if not using n_flux makes a mesh containing n_flux tag, and then
# makes a new tag called flux_tag, to use later in the test
flux_tag_name = "n_flux"
meshtal = Meshtal(
meshtal_file, {
4: (flux_tag_name, flux_tag_name + "_err",
flux_tag_name + "_total", flux_tag_name + "_err_total")
})
# Explicitly make this mesh unstructured, it will now iterate in yxz
# order which is MOAB structured mesh creation order.
meshtal = Mesh(structured=False, mesh=meshtal.tally[4].mesh)
meshtal_mesh_file = os.path.join(thisdir, "meshtal.h5m")
meshtal.write_hdf5(meshtal_mesh_file, write_mats=False)
new_mesh = Mesh(structured=False, mesh=meshtal_mesh_file)
new_mesh.TALLY_TAG = NativeMeshTag(2, float) # 2 egroups
new_mesh.TALLY_TAG = meshtal.n_flux[:]
# overwrite the mesh file
new_mesh.write_hdf5(meshtal_mesh_file, write_mats=False)
cell_mats = {
2:
Material({2004: 1.0}, density=1.0, metadata={'name': 'mat_11'}),
3:
Material({
3007: 0.4,
3006: 0.6
},
density=2.0,
metadata={'name': 'mat_12'})
}
alara_params = "Bogus line for testing\n"
geom = os.path.join(thisdir, "unitbox.h5m")
fluxin = os.path.join(os.getcwd(), "alara_fluxin")
reverse = True
alara_inp = os.path.join(os.getcwd(), "alara_inp")
alara_matlib = os.path.join(os.getcwd(), "alara_matlib")
output_mesh = os.path.join(os.getcwd(), "r2s_step1.h5m")
output_material = True
cell_fracs = np.zeros(4,
dtype=[('idx', np.int64), ('cell', np.int64),
('vol_frac', np.float64),
('rel_error', np.float64)])
cell_fracs[:] = [(0, 3, 1.0, 1.0), (1, 3, 1.0, 1.0), (2, 3, 1.0, 1.0),
(3, 3, 1.0, 1.0)]
irradiation_setup(flux_mesh=meshtal_mesh_file,
cell_mats=cell_mats,
cell_fracs=cell_fracs,
alara_params=alara_params,
flux_tag=flux_tag,
fluxin=fluxin,
reverse=reverse,
alara_inp=alara_inp,
alara_matlib=alara_matlib,
output_mesh=output_mesh,
output_material=output_material)
# expected output files
exp_alara_inp = os.path.join(thisdir, "files_test_r2s", "exp_alara_inp_un")
exp_alara_matlib = os.path.join(thisdir, "files_test_r2s",
"exp_alara_matlib")
exp_fluxin = os.path.join(thisdir, "files_test_r2s", "exp_fluxin_un")
# test files
f1 = filecmp.cmp(alara_inp, exp_alara_inp)
f2 = filecmp.cmp(alara_matlib, exp_alara_matlib)
f3 = filecmp.cmp(fluxin, exp_fluxin)
m = Mesh(structured=True, mesh=output_mesh, mats=output_mesh)
out = [
m.n_flux[:].tolist(), m.n_flux_err[:].tolist(),
m.n_flux_total[:].tolist(), m.n_flux_err_total[:].tolist(),
[x.comp.items() for y, x, z in m], [x.density for y, x, z in m]
]
n_flux = out[0]
n_flux_err = out[1]
n_flux_total = out[2]
n_flux_err_total = out[3]
densities = out[5]
comps = np.zeros(shape=(len(out[4])), dtype=dict)
for i, comp in enumerate(out[4]):
comps[i] = {}
for nucid in comp:
comps[i][nucid[0]] = nucid[1]
# test r2s step 1 output mesh
fluxes = [[6.93088E-07, 1.04838E-06], [6.36368E-07, 9.78475E-07],
[5.16309E-07, 9.86586E-07], [6.36887E-07, 9.29879E-07]]
errs = [[9.67452E-02, 7.55950E-02], [9.88806E-02, 7.61482E-02],
[1.04090E-01, 7.69284E-02], [9.75826E-02, 7.54181E-02]]
tot_fluxes = [1.74147E-06, 1.61484E-06, 1.50290E-06, 1.56677E-06]
tot_errs = [6.01522E-02, 6.13336E-02, 6.19920E-02, 5.98742E-02]
i = 0
for nf, nfe, nft, nfte, comp, density in izip(n_flux, n_flux_err,
n_flux_total,
n_flux_err_total, comps,
densities):
assert_almost_equal(density, 2.0)
assert_equal(len(comp), 2)
assert_almost_equal(comp[30060000], 0.6)
assert_almost_equal(comp[30070000], 0.4)
assert_array_equal(nf, fluxes[i])
assert_array_equal(nfe, errs[i])
assert_almost_equal(nft, tot_fluxes[i])
assert_almost_equal(nfte, tot_errs[i])
i += 1
os.remove(meshtal_mesh_file)
os.remove(alara_inp)
os.remove(alara_matlib)
os.remove(fluxin)
os.remove(output_mesh)
return [f1, f2, f3]
def irradiation_setup(flux_mesh, cell_mats, alara_params, tally_num=4,
geom=None, num_rays=10, grid=False, flux_tag="n_flux",
fluxin="alara_fluxin", reverse=False,
alara_inp="alara_geom", alara_matlib="alara_matlib",
output_mesh="r2s_step1.h5m", output_material=False):
"""This function is used to setup the irradiation inputs after the first
R2S transport step.
Parameters
----------
flux_mesh : PyNE Meshtal object, Mesh object, or str
The source of the neutron flux information. This can be a PyNE Meshtal
object, a pyne Mesh object, or the filename an MCNP meshtal file, or
the filename of an unstructured mesh tagged with fluxes.
tally_num : int
The MCNP FMESH4 tally number of the neutron flux tally within the
meshtal file.
cell_mats : dict
Maps geometry cell numbers to PyNE Material objects.
alara_params : str
The ALARA input blocks specifying everything except the geometry
and materials. This can either be passed as string or as a file name.
geom : str, optional
The file name of a DAGMC-loadable faceted geometry. This is only
necessary if the geometry is not already loaded into memory.
num_rays : int, optional
The number of rays to fire down a mesh row for geometry discretization.
This number must be a perfect square if grid=True.
grid : bool, optional
The if False, geometry discretization will be done with randomly fired
rays. If true, a grid of sqrt(num_rays) x sqrt(num_rays) rays is used
for each mesh row.
flux_tag : str, optional
The iMesh tag for the neutron flux.
fluxin : str, optional
The name of the ALARA fluxin file to be created.
reverse : bool, optional
If True the fluxes in the fluxin file will be printed in the reverse
order of how they appear within the flux vector tag. Since MCNP and
the Meshtal class order fluxes from low energy to high energy, this
option should only be true if the transmutation data being used is
ordered from high energy to low energy.
alara_inp : str, optional
The name of the ALARA input file to be created.
alara_matlib : str, optional
The name of the alara_matlib file to be created.
output_mesh : str, optional
A mesh containing all the fluxes and materials used for irradiation
setup.
output_material : bool, optional
If true, output mesh will have materials as determined by
dagmc.discretize_geom()
"""
from pyne.dagmc import load, discretize_geom
if geom is not None and isfile(geom):
load(geom)
# flux_mesh is Mesh object
if isinstance(flux_mesh, Mesh):
m = flux_mesh
# flux_mesh is unstructured mesh file
elif isinstance(flux_mesh, str) and isfile(flux_mesh) \
and flux_mesh.endswith(".h5m"):
m = Mesh(structured=False, mesh=flux_mesh)
# flux_mesh is Meshtal or meshtal file
else:
# flux_mesh is meshtal file
if isinstance(flux_mesh, str) and isfile(flux_mesh):
flux_mesh = Meshtal(flux_mesh,
{tally_num: (flux_tag, flux_tag + "_err",
flux_tag + "_total",
flux_tag + "_err_total")},
meshes_have_mats=output_material)
m = flux_mesh.tally[tally_num]
# flux_mesh is Meshtal object
elif isinstance(flux_mesh, Meshtal):
m = flux_mesh.tally[tally_num]
else:
raise ValueError("meshtal argument not a Mesh object, Meshtal"
" object, MCNP meshtal file or meshtal.h5m file.")
if m.structured:
cell_fracs = discretize_geom(m, num_rays=num_rays, grid=grid)
else:
cell_fracs = discretize_geom(m)
if output_material:
m.cell_fracs_to_mats(cell_fracs, cell_mats)
mesh_to_fluxin(m, flux_tag, fluxin, reverse)
record_to_geom(m, cell_fracs, cell_mats, alara_inp, alara_matlib)
if isfile(alara_params):
with open(alara_params, 'r') as f:
alara_params = f.read()
with open(alara_inp, 'a') as f:
f.write("\n" + alara_params)
m.write_hdf5(output_mesh)
def test_mesh_to_isotropic_source():
"""Test isotropic SOURCF generation."""
try:
from pyne import dagmc
except:
raise SkipTest
if not HAVE_PYMOAB:
raise SkipTest
m = Mesh(structured=True, structured_coords=[range(5), range(5), range(5)])
m.src = NativeMeshTag(4, float)
# These source values were carefully choosen so that:
# 1. The iteration order could be visually checked based on RTFLUX output using
# the resulting SOURCF card.
# 2. The repeation capability (i.e. 3R 0 = 0 0 0) could be tested.
m.src[:] = [
[0, 0, 0, 100],
[0, 0, 0, 0],
[0, 0, 0, 6],
[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, 0],
[0, 0, 100, 0],
[0, 0, 0, 5],
[0, 0, 0, 6],
[0, 0, 0, 0],
[0, 0, 0, 8],
[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, 100, 0, 0],
[0, 0, 0, 5],
[0, 0, 0, 0],
[0, 0, 0, 7],
[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],
[100, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 7],
[0, 0, 0, 8],
[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],
]
out = partisn.mesh_to_isotropic_source(m, "src")
exp = (
"sourcf= 1.00000E+02 3R 0; 0 8.00000E+00 0 8.00000E+00; 4R 0; 4R 0; 0 5.00000E+00\n"
"5.00000E+00 0; 4R 0; 4R 0; 4R 0; 6.00000E+00 6.00000E+00 2R 0; 4R 0; 4R 0; 4R 0;\n"
"2R 0 7.00000E+00 7.00000E+00; 4R 0; 4R 0; 4R 0; 0 1.00000E+02 2R 0; 4R 0; 4R 0;\n"
"4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 2R\n"
"0 1.00000E+02 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R\n"
"0; 4R 0; 4R 0; 4R 0; 4R 0; 3R 0 1.00000E+02; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0;\n"
"4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0; 4R 0;")
assert out == exp
def test_issue360():
a = Mesh(structured=True, structured_coords=[[0, 1, 2], [0, 1], [0, 1]])
a.cat = NativeMeshTag(3, float)
a.cat[:] = [[0.11, 0.22, 0.33], [0.44, 0.55, 0.66]]
a.cat[:] = np.array([[0.11, 0.22, 0.33], [0.44, 0.55, 0.66]])
def get_zones_with_void():
"""Test the _get_zones function if a void is present."""
try:
from pyne import dagmc
except:
raise SkipTest
if not HAVE_PYMOAB:
raise SkipTest
# hdf5 test file
THIS_DIR = os.path.dirname(os.path.realpath(__file__))
hdf5 = THIS_DIR + "/files_test_partisn/partisn_test_geom.h5m"
data_hdf5path = "/materials"
dagmc.load(hdf5)
# mesh
xvals = [-5.0, 0.0, 10.0, 15.0, 15.1]
yvals = [-5.0, 0.0, 5.0]
zvals = [-5.0, 0.0, 5.0]
mesh = Mesh(
structured_coords=[xvals, yvals, zvals],
structured=True,
structured_ordering="xyz",
)
# more inputs
bounds = {"x": xvals, "y": yvals, "z": zvals}
num_rays = 400
grid = True
dg = None
mat_assigns = None
unique_names = {
"mat:Helium, Natural": "HELIUMNA",
"mat:Mercury": "MERCURY1"
}
voxel_zones, zones = partisn._get_zones(mesh, hdf5, bounds, num_rays, grid,
dg, mat_assigns, unique_names)
# expected results
voxel_zones_expected = np.array([[1, 1, 1, 1], [2, 2, 2, 2], [3, 3, 3, 3],
[0, 0, 0, 0]])
zones_expected = {
1: {
"vol_frac": [1.0],
"mat": ["HELIUMNA"]
},
2: {
"vol_frac": [0.5, 0.5],
"mat": ["HELIUMNA", "MERCURY1"]
},
3: {
"vol_frac": [1.0],
"mat": ["MERCURY1"]
},
}
vz_tf = False
z_tf = False
if voxel_zones.all() == voxel_zones_expected.all():
vz_tf = True
if zones == zones_expected:
z_tf = True
# assert(voxel_zones.all() == voxel_zones_expected.all())
# assert(zones == zones_expected)
return [vz_tf, z_tf]
def test_unstructured_mesh_from_file():
filename = os.path.join(os.path.dirname(__file__),
"files_mesh_test/unstr.h5m")
sm = Mesh(mesh=filename)
def test_wwinp_np():
if not HAVE_PYMOAB:
raise SkipTest
thisdir = os.path.dirname(__file__)
wwinp_file = os.path.join(thisdir, 'mcnp_wwinp_wwinp_np.txt')
expected_h5m = os.path.join(thisdir, 'mcnp_wwinp_mesh_np.h5m')
expected_sm = Mesh(mesh=expected_h5m, structured=True)
output = os.path.join(os.getcwd(), 'test_wwinp')
# Read in the wwinp file to an object and check resulting attributes.
ww1 = mcnp.Wwinp()
ww1.read_wwinp(wwinp_file)
assert_equal(ww1.ni, 2)
assert_equal(ww1.nr, 10)
assert_equal(ww1.ne, [7, 1])
assert_equal(ww1.nf, [1, 8, 6])
assert_equal(ww1.origin, [-100, -100, -100])
assert_equal(ww1.nc, [1, 3, 1])
assert_equal(ww1.nwg, 1)
assert_equal(ww1.cm, [[100], [-50, 60, 100], [100]])
assert_equal(ww1.fm, [[1], [1, 3, 4], [6]])
assert_equal(ww1.e[0],
[0.1, 0.14678, 0.21544, 0.31623, 0.46416, 0.68129, 1.0000])
assert_array_equal(ww1.e[1], [100])
assert_equal(ww1.bounds,
[[-100.0, 100],
[
-100.0, -50.0, -13.333333333333336, 23.333333333333329,
60.0, 70.0, 80.0, 90.0, 100.0
],
[
-100.0, -66.666666666666657, -33.333333333333329, 0.0,
33.333333333333343, 66.666666666666657, 100.0
]])
expected_ves = list(expected_sm.structured_iterate_hex("zyx"))
written_ves = list(expected_sm.structured_iterate_hex("zyx"))
for expected_ve, written_ve in zip(expected_ves, written_ves):
expected = expected_sm.ww_n[expected_ve]
written = ww1.ww_n[written_ve]
assert_array_equal(written, expected)
expected_ves = list(expected_sm.structured_iterate_hex("zyx"))
written_ves = list(expected_sm.structured_iterate_hex("zyx"))
for expected_ve, written_ve in zip(expected_ves, written_ves):
expected = expected_sm.ww_p[expected_ve]
written = ww1.ww_p[written_ve]
assert_array_equal(written, expected)
# Create an new object based off of only the mesh attribute of the first
# object and check resutling attributes.
ww2 = mcnp.Wwinp()
ww2.read_mesh(ww1.mesh)
assert_equal(ww2.ni, 2)
assert_equal(ww2.nr, 10)
assert_equal(ww2.ne, [7, 1])
assert_equal(ww2.nf, [1, 8, 6])
assert_equal(ww2.origin, [-100, -100, -100])
assert_equal(ww2.nc, [1, 3, 1])
assert_equal(ww2.nwg, 1)
assert_equal(ww2.cm, [[100], [-50, 60, 100], [100]])
assert_equal(ww2.fm, [[1], [1, 3, 4], [6]])
assert_array_equal(
ww2.e[0], [0.1, 0.14678, 0.21544, 0.31623, 0.46416, 0.68129, 1.0000])
assert_array_equal(ww2.e[1], [100])
assert_equal(ww2.bounds,
[[-100.0, 100],
[
-100.0, -50.0, -13.333333333333336, 23.333333333333329,
60.0, 70.0, 80.0, 90.0, 100.0
],
[
-100.0, -66.666666666666657, -33.333333333333329, 0.0,
33.333333333333343, 66.666666666666657, 100.0
]])
expected_ves = list(expected_sm.structured_iterate_hex("zyx"))
written_ves = list(expected_sm.structured_iterate_hex("zyx"))
for expected_ve, written_ve in zip(expected_ves, written_ves):
expected = expected_sm.ww_n[expected_ve]
written = ww2.ww_n[written_ve]
assert_array_equal(written, expected)
expected_ves = list(expected_sm.structured_iterate_hex("zyx"))
written_ves = list(expected_sm.structured_iterate_hex("zyx"))
for expected_ve, written_ve in zip(expected_ves, written_ves):
expected = expected_sm.ww_p[expected_ve]
written = ww2.ww_p[written_ve]
assert_array_equal(written, expected)
# write a new wwinp file and verify that is same wwinp file used as an
# input to this test
ww2.write_wwinp(output)
expected_output = wwinp_file
with open(output) as f:
written = f.readlines()
with open(expected_output) as f:
expected = f.readlines()
# check to make sure file are the same except for the data/time info
# on line 1
assert_equal(written[0].split()[:-2], expected[0].split()[:-2])
assert_equal(len(written), len(expected))
for i in range(1, len(expected)):
for j in range(0, len(expected[i].split())):
assert_equal(float(written[i].split()[j]),
float(expected[i].split()[j]))
os.remove(output)
def test_tag_e_bounds():
m = Mesh(structured=True, structured_coords=[[0, 1, 2], [0, 1, 3], [0, 1]])
e_bounds = np.array([0.0, 0.1, 20])
m = tag_e_bounds(m, e_bounds)
assert_array_equal(m.e_bounds[m], e_bounds)
def test_irradiation_setup_structured():
meshtal = os.path.join(thisdir, "files_test_r2s", "meshtal_2x2x1")
tally_num = 4
cell_mats = {
2: Material({2004: 1.0}, density=1.0),
3: Material({
3007: 0.4,
3006: 0.6
}, density=2.0)
}
alara_params = "Bogus line for testing"
geom = os.path.join(thisdir, "unitbox.h5m")
num_rays = 9
grid = True
flux_tag = "n_flux"
fluxin = os.path.join(os.getcwd(), "alara_fluxin")
reverse = True
alara_inp = os.path.join(os.getcwd(), "alara_inp")
alara_matlib = os.path.join(os.getcwd(), "alara_matlib")
output_mesh = os.path.join(os.getcwd(), "r2s_step1.h5m")
irradiation_setup(meshtal, cell_mats, alara_params, tally_num, geom,
num_rays, grid, flux_tag, fluxin, reverse, alara_inp,
alara_matlib, output_mesh)
# expected output files
exp_alara_inp = os.path.join(thisdir, "files_test_r2s", "exp_alara_inp")
exp_alara_matlib = os.path.join(thisdir, "files_test_r2s",
"exp_alara_matlib")
exp_fluxin = os.path.join(thisdir, "files_test_r2s", "exp_fluxin")
# test alara input file
with open(alara_inp, 'r') as f1, open(exp_alara_inp, 'r') as f2:
for a, b in zip(f1.readlines(), f2.readlines()):
assert_equal(a, b)
# test alara matlibe file
with open(alara_matlib, 'r') as f1, open(exp_alara_matlib) as f2:
for a, b in zip(f1.readlines(), f2.readlines()):
assert_equal(a, b)
# test alara fluxin file
with open(fluxin, 'r') as f1, open(exp_fluxin) as f2:
for a, b in zip(f1.readlines(), f2.readlines()):
assert_equal(a, b)
# test r2s step 1 output mesh
fluxes = [[6.93088E-07, 1.04838E-06], [6.36368E-07, 9.78475E-07],
[5.16309E-07, 9.86586E-07], [6.36887E-07, 9.29879E-07]]
errs = [[9.67452E-02, 7.55950E-02], [9.88806E-02, 7.61482E-02],
[1.04090E-01, 7.69284E-02], [9.75826E-02, 7.54181E-02]]
tot_fluxes = [1.74147E-06, 1.61484E-06, 1.50290E-06, 1.56677E-06]
tot_errs = [6.01522E-02, 6.13336E-02, 6.19920E-02, 5.98742E-02]
m = Mesh(structured=True, mesh=output_mesh, mats=output_mesh)
for i, mat, _ in m:
assert_almost_equal(mat.density, 1.962963E+00)
assert_equal(len(mat.comp), 3)
assert_almost_equal(mat.comp[20040000], 1.886792E-02)
assert_almost_equal(mat.comp[30060000], 5.886792E-01)
assert_almost_equal(mat.comp[30070000], 3.924528E-01)
assert_array_equal(m.n_flux[i], fluxes[i])
assert_array_equal(m.n_flux_err[i], errs[i])
assert_almost_equal(m.n_flux_total[i], tot_fluxes[i])
assert_almost_equal(m.n_flux_err_total[i], tot_errs[i])
os.remove(alara_inp)
os.remove(alara_matlib)
os.remove(fluxin)
os.remove(output_mesh)
def test_write_fluxin_multiple_subvoxel():
"""This function tests the flux_mesh_to_fluxin function for a multiple
energy group case under sub-voxel r2s.
"""
if not HAVE_PYMOAB:
raise SkipTest
output_name = "fluxin_subvoxel.out"
forward_fluxin = os.path.join(thisdir, "files_test_alara",
"fluxin_multiple_forward_subvoxel.txt")
reverse_fluxin = os.path.join(thisdir, "files_test_alara",
"fluxin_multiple_reverse_subvoxel.txt")
output = os.path.join(os.getcwd(), output_name)
flux_mesh = Mesh(structured=True,
structured_coords=[[0, 1, 2], [0, 1, 2], [0, 1]])
flux_data = [[1, 2, 3, 4, 5, 6, 7], [8, 9, 10, 11, 12, 13, 14],
[15, 16, 17, 18, 19, 20, 21], [22, 23, 24, 25, 26, 27, 28]]
flux_mesh.tag("flux", flux_data, 'nat_mesh', size=7, dtype=float)
cell_fracs = np.zeros(6,
dtype=[('idx', np.int64), ('cell', np.int64),
('vol_frac', np.float64),
('rel_error', np.float64)])
cell_fracs[:] = [(0, 11, 1, 0.0), (1, 11, 0.5, 0.0), (1, 12, 0.5, 0.0),
(2, 11, 0.5, 0.0), (2, 13, 0.5, 0.0), (3, 13, 1, 0.0)]
cell_mats = {
11: Material({'H': 1.0}, density=1.0),
12: Material({'He': 1.0}, density=1.0),
13: Material({}, density=0.0, metadata={'name': 'void'})
}
# test forward writting
mesh_to_fluxin(flux_mesh, "flux", output_name, False, True, cell_fracs,
cell_mats)
with open(output) as f:
written = f.readlines()
with open(forward_fluxin) as f:
expected = f.readlines()
assert_equal(written, expected)
if os.path.isfile(output):
os.remove(output)
# test reverse writting
mesh_to_fluxin(flux_mesh, "flux", output_name, True, True, cell_fracs,
cell_mats)
with open(output) as f:
written = f.readlines()
with open(reverse_fluxin) as f:
expected = f.readlines()
assert_equal(written, expected)
if os.path.isfile(output):
os.remove(output)
def test_tag_source_intensity():
m = Mesh(structured=True, structured_coords=[[0, 1, 2], [0, 1, 3], [0, 1]])
source_intensity = 1.0
m = tag_source_intensity(m, source_intensity)
assert_array_equal(m.source_intensity[m], source_intensity)
class TestArithmetic():
def arithmetic_mesh_setup(self):
self.mesh_1 = Mesh(structured_coords=[[-1, 0, 1], [-1, 0, 1], [0, 1]],
structured=True)
volumes1 = list(self.mesh_1.structured_iterate_hex("xyz"))
volumes2 = list(self.mesh_1.structured_iterate_hex("xyz"))
flux_tag = self.mesh_1.mesh.tag_get_handle("flux",
1,
types.MB_TYPE_DOUBLE,
types.MB_TAG_DENSE,
create_if_missing=True)
flux_data = [1.0, 2.0, 3.0, 4.0]
self.mesh_1.mesh.tag_set_data(flux_tag, volumes1, flux_data)
self.mesh_2 = Mesh(structured_coords=[[-1, 0, 1], [-1, 0, 1], [0, 1]],
structured=True)
volumes1 = list(self.mesh_2.structured_iterate_hex("xyz"))
volumes2 = list(self.mesh_2.structured_iterate_hex("xyz"))
flux_tag = self.mesh_2.mesh.tag_get_handle("flux",
1,
types.MB_TYPE_DOUBLE,
types.MB_TAG_DENSE,
create_if_missing=True)
flux_data = [1.1, 2.2, 3.3, 4.4]
self.mesh_2.mesh.tag_set_data(flux_tag, volumes1, flux_data)
def arithmetic_statmesh_setup(self):
self.statmesh_1 = StatMesh(structured_coords=[[-1, 0, 1], [-1, 0, 1],
[0, 1]],
structured=True)
volumes1 = list(self.statmesh_1.structured_iterate_hex("xyz"))
volumes2 = list(self.statmesh_1.structured_iterate_hex("xyz"))
flux_tag = self.statmesh_1.mesh.tag_get_handle("flux",
1,
types.MB_TYPE_DOUBLE,
types.MB_TAG_DENSE,
create_if_missing=True)
error_tag = self.statmesh_1.mesh.tag_get_handle("flux_rel_error",
1,
types.MB_TYPE_DOUBLE,
types.MB_TAG_DENSE,
create_if_missing=True)
flux_data = [1.0, 2.0, 3.0, 4.0]
error_data = [0.1, 0.2, 0.3, 0.4]
self.statmesh_1.mesh.tag_set_data(flux_tag, volumes1, flux_data)
self.statmesh_1.mesh.tag_set_data(error_tag, volumes2, error_data)
self.statmesh_2 = StatMesh(structured_coords=[[-1, 0, 1], [-1, 0, 1],
[0, 1]],
structured=True)
volumes1 = list(self.statmesh_2.structured_iterate_hex("xyz"))
volumes2 = list(self.statmesh_2.structured_iterate_hex("xyz"))
flux_tag = self.statmesh_2.mesh.tag_get_handle("flux",
1,
types.MB_TYPE_DOUBLE,
types.MB_TAG_DENSE,
create_if_missing=True)
error_tag = self.statmesh_2.mesh.tag_get_handle("flux_rel_error",
1,
types.MB_TYPE_DOUBLE,
types.MB_TAG_DENSE,
create_if_missing=True)
flux_data = [1.1, 2.2, 3.3, 4.4]
error_data = [0.1, 0.2, 0.3, 0.4]
self.statmesh_2.mesh.tag_set_data(flux_tag, volumes1, flux_data)
self.statmesh_2.mesh.tag_set_data(error_tag, volumes2, error_data)
def test_add_mesh(self):
self.arithmetic_mesh_setup()
self.mesh_1 += self.mesh_2
exp_res = [2.1, 4.2, 6.3, 8.4]
flux_tag = self.mesh_1.mesh.tag_get_handle("flux")
obs_res = [
self.mesh_1.mesh.tag_get_data(flux_tag, vol, flat=True)[0]
for vol in self.mesh_1.structured_iterate_hex("xyz")
]
assert_array_almost_equal(exp_res, obs_res)
def test_subtract_mesh(self):
self.arithmetic_mesh_setup()
self.mesh_1 -= self.mesh_2
exp_res = [-0.1, -0.2, -0.3, -0.4]
flux_tag = self.mesh_1.mesh.tag_get_handle("flux")
obs_res = [
self.mesh_1.mesh.tag_get_data(flux_tag, vol, flat=True)[0]
for vol in self.mesh_1.structured_iterate_hex("xyz")
]
assert_array_almost_equal(exp_res, obs_res)
def test_multiply_mesh(self):
self.arithmetic_mesh_setup()
self.mesh_1 *= self.mesh_2
exp_res = [1.1, 4.4, 9.9, 17.6]
flux_tag = self.mesh_1.mesh.tag_get_handle("flux")
obs_res = [
self.mesh_1.mesh.tag_get_data(flux_tag, vol, flat=True)[0]
for vol in self.mesh_1.structured_iterate_hex("xyz")
]
assert_array_almost_equal(exp_res, obs_res)
def test_divide_mesh(self):
self.arithmetic_mesh_setup()
self.mesh_1 /= self.mesh_2
exp_res = [0.9090909091, 0.9090909091, 0.9090909091, 0.9090909091]
flux_tag = self.mesh_1.mesh.tag_get_handle("flux")
obs_res = [
self.mesh_1.mesh.tag_get_data(flux_tag, vol, flat=True)[0]
for vol in self.mesh_1.structured_iterate_hex("xyz")
]
assert_array_almost_equal(exp_res, obs_res)
def test_add_statmesh(self):
self.arithmetic_statmesh_setup()
self.statmesh_1 += self.statmesh_2
exp_res = [2.1, 4.2, 6.3, 8.4]
exp_err = [
0.070790803558659549, 0.1415816071173191, 0.21237241067597862,
0.28316321423463819
]
flux_tag = self.statmesh_1.mesh.tag_get_handle("flux")
obs_res = [
self.statmesh_1.mesh.tag_get_data(flux_tag, vol, flat=True)[0]
for vol in self.statmesh_1.structured_iterate_hex("xyz")
]
flux_err_tag = self.statmesh_1.mesh.tag_get_handle("flux_rel_error")
obs_err = [
self.statmesh_1.mesh.tag_get_data(flux_err_tag, vol, flat=True)[0]
for vol in self.statmesh_1.structured_iterate_hex("xyz")
]
assert_array_almost_equal(exp_res, obs_res)
assert_array_almost_equal(exp_err, obs_err)
def test_subtract_statmesh(self):
self.arithmetic_statmesh_setup()
self.statmesh_1 -= self.statmesh_2
exp_res = [-0.1, -0.2, -0.3, -0.4]
exp_err = [-1.4866068747, -2.9732137495, -4.4598206242, -5.9464274989]
flux_tag = self.statmesh_1.mesh.tag_get_handle("flux")
obs_res = [
self.statmesh_1.mesh.tag_get_data(flux_tag, vol, flat=True)[0]
for vol in self.statmesh_1.structured_iterate_hex("xyz")
]
flux_err_tag = self.statmesh_1.mesh.tag_get_handle("flux_rel_error")
obs_err = [
self.statmesh_1.mesh.tag_get_data(flux_err_tag, vol, flat=True)[0]
for vol in self.statmesh_1.structured_iterate_hex("xyz")
]
assert_array_almost_equal(exp_res, obs_res)
assert_array_almost_equal(exp_err, obs_err)
def test_multiply_statmesh(self):
self.arithmetic_statmesh_setup()
self.statmesh_1 *= self.statmesh_2
exp_res = [1.1, 4.4, 9.9, 17.6]
exp_err = [
0.1414213562,
0.2828427125,
0.4242640687,
0.5656854249,
]
flux_tag = self.statmesh_1.mesh.tag_get_handle("flux")
obs_res = [
self.statmesh_1.mesh.tag_get_data(flux_tag, vol, flat=True)[0]
for vol in self.statmesh_1.structured_iterate_hex("xyz")
]
flux_err_tag = self.statmesh_1.mesh.tag_get_handle("flux_rel_error")
obs_err = [
self.statmesh_1.mesh.tag_get_data(flux_err_tag, vol, flat=True)[0]
for vol in self.statmesh_1.structured_iterate_hex("xyz")
]
assert_array_almost_equal(exp_res, obs_res)
assert_array_almost_equal(exp_err, obs_err)
def test_divide_statmesh(self):
self.arithmetic_statmesh_setup()
self.statmesh_1 /= self.statmesh_2
exp_res = [0.9090909091, 0.9090909091, 0.9090909091, 0.9090909091]
exp_err = [0.1414213562, 0.2828427125, 0.4242640687, 0.5656854249]
flux_tag = self.statmesh_1.mesh.tag_get_handle("flux")
obs_res = [
self.statmesh_1.mesh.tag_get_data(flux_tag, vol, flat=True)[0]
for vol in self.statmesh_1.structured_iterate_hex("xyz")
]
flux_err_tag = self.statmesh_1.mesh.tag_get_handle("flux_rel_error")
obs_err = [
self.statmesh_1.mesh.tag_get_data(flux_err_tag, vol, flat=True)[0]
for vol in self.statmesh_1.structured_iterate_hex("xyz")
]
assert_array_almost_equal(exp_res, obs_res)
assert_array_almost_equal(exp_err, obs_err)
def test_single_meshtally_meshtal():
"""Test a meshtal file containing a single mesh tally.
"""
if not HAVE_PYMOAB:
raise SkipTest
thisdir = os.path.dirname(__file__)
meshtal_file = os.path.join(thisdir, "mcnp_meshtal_single_meshtal.txt")
expected_h5m = os.path.join(thisdir, "mcnp_meshtal_single_mesh.h5m")
expected_sm = Mesh(mesh=expected_h5m, structured=True)
tags = {
4: ["n_result", "n_rel_error", "n_total_result", "n_total_rel_error"]
}
meshtal_object = mcnp.Meshtal(meshtal_file, tags, meshes_have_mats=True)
assert_not_equal(meshtal_object.tally[4].mats, None)
# test Meshtal attributes
assert_equal(meshtal_object.version, '5.mpi')
assert_equal(meshtal_object.ld, "09282010")
assert_equal(meshtal_object.title,
"Input file to general test meshtal file")
assert_equal(meshtal_object.histories, 100000)
# test MeshTally attributes
assert_equal(meshtal_object.tally[4].tally_number, 4)
assert_equal(meshtal_object.tally[4].particle, "neutron")
assert_equal(meshtal_object.tally[4].dose_response, True)
assert_equal(meshtal_object.tally[4].x_bounds,
[-200.00, -66.67, 66.67, 200.00])
assert_equal(meshtal_object.tally[4].y_bounds,
[-200.00, -120.00, -40.00, 40.00, 120.00, 200.00])
assert_equal(meshtal_object.tally[4].z_bounds,
[-200.00, -50.00, 100.00, 200.00])
assert_equal(meshtal_object.tally[4].e_bounds,
[0.00E+00, 1.00E-01, 2.00E-01, 1.00E+00])
# test vector tags
for v_e, expected_v_e in zip(
meshtal_object.tally[4].structured_iterate_hex("xyz"),
expected_sm.structured_iterate_hex("xyz")):
written = meshtal_object.tally[4].n_result[v_e]
expected = expected_sm.n_result[expected_v_e]
assert_array_equal(written, expected)
for v_e, expected_v_e in zip(
meshtal_object.tally[4].structured_iterate_hex("xyz"),
expected_sm.structured_iterate_hex("xyz")):
written = meshtal_object.tally[4].n_rel_error[v_e]
expected = expected_sm.n_rel_error[expected_v_e]
assert_array_equal(written, expected)
# test total tag
for v_e, expected_v_e in zip(
meshtal_object.tally[4].structured_iterate_hex("xyz"),
expected_sm.structured_iterate_hex("xyz")):
written = meshtal_object.tally[4].n_total_result[v_e]
expected = expected_sm.n_total_result[expected_v_e]
assert_equal(written, expected)
for v_e, expected_v_e in zip(
meshtal_object.tally[4].structured_iterate_hex("xyz"),
expected_sm.structured_iterate_hex("xyz")):
written = meshtal_object.tally[4].n_total_rel_error[v_e]
expected = expected_sm.n_total_rel_error[expected_v_e]
assert_equal(written, expected)
def step1(cfg):
""" This function writes the PARTISN input file for the adjoint photon
transport
Parameters
----------
cfg : dictionary
User input for step 1 from the config.yml file
"""
# Get user-input from config file
geom = cfg['geom_file']
cells = [cfg['src_cell']]
src_vol = [float(cfg['src_vol'])]
try:
origin_x, origin_y, origin_z = cfg['origin'].split(' ')
except:
print("Too few entries in origin location")
xmesh = cfg['xmesh']
xints = cfg['xints']
ymesh = cfg['ymesh']
yints = cfg['yints']
zmesh = cfg['zmesh']
zints = cfg['zints']
# Create structured mesh
sc = [
np.linspace(float(origin_x), float(xmesh),
float(xints) + 1),
np.linspace(float(origin_y), float(ymesh),
float(yints) + 1),
np.linspace(float(origin_z), float(zmesh),
float(zints) + 1)
]
m = Mesh(structured=True, structured_coords=sc)
m.write_hdf5("blank_mesh.h5m")
# Generate 42 photon energy bins [eV]
# First bin has been replaced with 1 for log interpolation
photon_bins = np.array([
1e-6, 0.01, 0.02, 0.03, 0.045, 0.06, 0.07, 0.075, 0.1, 0.15, 0.2, 0.3,
0.4, 0.45, 0.51, 0.512, 0.6, 0.7, 0.8, 1, 1.33, 1.34, 1.5, 1.66, 2,
2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 10, 12, 14, 20, 30, 50
])
# ICRP 74 flux-to-dose conversion factors in pico-Sv/s per photon flux
de = np.array([
0.01, 0.015, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.1, 0.15, 0.2,
0.3, 0.4, 0.5, 0.6, 0.8, 1, 2, 4, 6, 8, 10
])
df = np.array([
0.0485, 0.1254, 0.205, 0.2999, 0.3381, 0.3572, 0.378, 0.4066, 0.4399,
0.5172, 0.7523, 1.0041, 1.5083, 1.9958, 2.4657, 2.9082, 3.7269, 4.4834,
7.4896, 12.0153, 15.9873, 19.9191, 23.76
])
# Convert to Sv/s per photon FLUX
pico = 1.0e-12
df = df * pico
# Convert pointwise data to group data for log interpolation
photon_spectrum = pointwise_collapse(photon_bins,
de,
df,
logx=True,
logy=True)
# Anything below 0.01 MeV should be assigned the DF value of 0.01 MeV
photon_spectrum[0] = df[0]
# Total number of groups is 217 (42 photon + 175 neutron)
spectra = [np.append(photon_spectrum, np.zeros(175))]
# The spectrum is normalized by PyNE, so we need to mutliply by the sum of
# intensities in the spectrum.
# Additionally, we divide by the volume of the source cell in order to get
# source density.
intensities = [np.sum(spectra) / src_vol]
# Load geometry into DAGMC
load(geom)
# Generate isotropic photon volume source
source, dg = isotropic_vol_source(geom, m, cells, spectra, intensities)
# PARTISN input
ngroup = 217 # total number of energy groups
cards = _cards(source) # block 1, 3, 5 input values
names_dict = _names_dict(
) # dictionary of isotopes (PyNE nucids to bxslib names)
write_partisn_input(m,
geom,
ngroup,
cards=cards,
dg=dg,
names_dict=names_dict,
data_hdf5path="/materials",
nuc_hdf5path="/nucid",
fine_per_coarse=1)
def test_record_to_geom_subvoxel():
if not HAVE_PYMOAB:
raise SkipTest
expected_geom = os.path.join(thisdir, "files_test_alara",
"alara_record_geom_subvoxel.txt")
expected_matlib = os.path.join(thisdir, "files_test_alara",
"alara_record_matlib_subvoxel.txt")
geom = os.path.join(os.getcwd(), "alara_record_geom")
matlib = os.path.join(os.getcwd(), "alara_record_matlib")
cell_fracs = np.zeros(11,
dtype=[('idx', np.int64), ('cell', np.int64),
('vol_frac', np.float64),
('rel_error', np.float64)])
cell_mats = {
11:
Material({
'H1': 1.0,
'K39': 1.0
},
density=1.1,
metadata={'name': 'fake_mat'}),
12:
Material({
'H1': 0.1,
'O16': 1.0
},
density=1.2,
metadata={'name': 'water'}),
13:
Material({'He4': 42.0}, density=1.3, metadata={'name': 'helium'}),
14:
Material({}, density=0.0, metadata={'name': 'void'}),
15:
Material({}, density=0.0, metadata={'name': 'void'}),
16:
Material({
'H1': 1.0,
'K39': 1.0
},
density=1.1,
metadata={'name': 'fake_mat'})
}
cell_fracs[:] = [(0, 11, 0.55, 0.0), (0, 12, 0.45, 0.0), (1, 11, 0.2, 0.0),
(1, 12, 0.3, 0.0), (1, 13, 0.5, 0.0), (2, 11, 0.15, 0.0),
(2, 14, 0.01, 0.0), (2, 15, 0.04, 0.0), (2, 16, 0.8, 0.0),
(3, 11, 0.55, 0.0), (3, 12, 0.45, 0.0)]
m = Mesh(structured_coords=[[-1, 0, 1], [-1, 0, 1], [0, 1]],
structured=True,
mats=None)
record_to_geom(m, cell_fracs, cell_mats, geom, matlib, sub_voxel=True)
assert (filecmp.cmp(geom, expected_geom))
if os.path.isfile(geom):
os.remove(geom)
assert (filecmp.cmp(matlib, expected_matlib))
if os.path.isfile(matlib):
os.remove(matlib)
def test_tag_decay_time():
m = Mesh(structured=True, structured_coords=[[0, 1, 2], [0, 1, 3], [0, 1]])
decay_time = 1.0
m = tag_decay_time(m, decay_time)
assert_array_equal(m.decay_time[m], decay_time)