def boundary():
from pyne import dagmc
dagmc.load(path)
low, high = dagmc.volume_boundary(2)
return [low, high]
def versions():
from pyne import dagmc
dagmc.load(path)
returned = dagmc.versions()
return returned
def ray_iterator():
from pyne import dagmc
dagmc.load(path)
start = [-2, 0, 0]
startvol = dagmc.find_volume(start)
assert_equal(startvol, 3)
direction = [1, 0, 0]
expected_vols = [2, 3, 1, 4]
expected_dists = [1, 2, 3.156921938, 0]
for i, (vol, dist, surf) in enumerate(
dagmc.ray_iterator(startvol, start, direction)):
assert_equal(expected_vols[i], vol)
if expected_dists[i] != 0:
assert_almost_equal(expected_dists[i], dist)
assert_equal(i, 3)
for i, (vol, dist, surf) in enumerate(
dagmc.ray_iterator(startvol, start, direction, dist_limit=4)):
assert_equal(expected_vols[i], vol)
if expected_dists[i] != 0:
assert_almost_equal(expected_dists[i], dist)
assert_equal(i, 1)
def failures():
from pyne import dagmc
dagmc.load(path)
assert_raises(Exception, dagmc.point_in_volume, [100, (0, 0, 0)])
assert_raises(Exception, dagmc.point_in_volume, [1, (0, 0, 0, 0)])
assert_raises(Exception, dagmc.fire_one_ray, [2, (0, 0, 0), 1])
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'
# 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 failures():
from pyne import dagmc
dagmc.load(path)
assert_raises(Exception, dagmc.point_in_volume, [100, (0, 0, 0)])
assert_raises(Exception, dagmc.point_in_volume, [1, (0, 0, 0, 0)])
assert_raises(Exception, dagmc.fire_one_ray, [2, (0, 0, 0), 1])
def ray_iterator():
from pyne import dagmc
dagmc.load(path)
start = [-2, 0, 0]
startvol = dagmc.find_volume(start)
direction = [1, 0, 0]
expected_vols = [2, 3, 1, 4]
expected_dists = [1, 2, 3.156921938, 0]
vols1 = []
dists1 = []
surfs1 = []
for i, (vol, dist,
surf) in enumerate(dagmc.ray_iterator(startvol, start, direction)):
vols1.append(vol)
dists1.append(dist)
surfs1.append(surf)
vols2 = []
dists2 = []
surfs2 = []
for j, (vol, dist, surf) in enumerate(
dagmc.ray_iterator(startvol, start, direction, dist_limit=4)):
vols2.append(vol)
dists2.append(dist)
surfs2.append(surf)
return [startvol, vols1, dists1, surfs1, i, vols2, dists2, surfs2, j]
def step1():
config = ConfigParser.ConfigParser()
config.read(config_filename)
structured = config.getboolean("general", "structured")
sub_voxel = config.getboolean("general", "sub_voxel")
meshtal = config.get("step1", "meshtal")
tally_num = config.getint("step1", "tally_num")
flux_tag = config.get("step1", "flux_tag")
decay_times = config.get("step2", "decay_times").split(",")
geom = config.get("step1", "geom")
reverse = config.getboolean("step1", "reverse")
num_rays = config.getint("step1", "num_rays")
grid = config.getboolean("step1", "grid")
load(geom)
# get meshtal info from meshtal file
flux_mesh = resolve_mesh(meshtal, tally_num, flux_tag)
# create the cell_fracs array before irradiation_steup
if flux_mesh.structured:
cell_fracs = discretize_geom(flux_mesh, num_rays=num_rays, grid=grid)
# tag cell fracs for both default and subvoxel r2s modes
flux_mesh.tag_cell_fracs(cell_fracs)
else:
cell_fracs = discretize_geom(flux_mesh)
cell_mats = cell_materials(geom)
irradiation_setup(
flux_mesh,
cell_mats,
cell_fracs,
alara_params_filename,
tally_num,
num_rays=num_rays,
grid=grid,
reverse=reverse,
flux_tag=flux_tag,
decay_times=decay_times,
sub_voxel=sub_voxel,
)
# create a blank mesh for step 2:
ves = list(flux_mesh.iter_ve())
tags_keep = (
"cell_number",
"cell_fracs",
"cell_largest_frac_number",
"cell_largest_frac",
)
for tag in flux_mesh.get_all_tags():
if tag.name not in tags_keep and isinstance(tag, NativeMeshTag):
tag.delete()
flux_mesh.write_hdf5("blank_mesh.h5m")
print("The file blank_mesh.h5m has been saved to disk.")
print("Do not delete this file; it is needed by r2s.py step2.\n")
print("R2S step1 complete, run ALARA with the command:")
print(">> alara alara_inp > output.txt")
def ray_iterator():
from pyne import dagmc
dagmc.load(path)
start = [-2, 0, 0]
startvol = dagmc.find_volume(start)
assert_equal(startvol, 3)
direction = [1, 0, 0]
expected_vols = [2, 3, 1, 4]
expected_dists = [1, 2, 3.156921938, 0]
for i, (vol, dist,
surf) in enumerate(dagmc.ray_iterator(startvol, start, direction)):
assert_equal(expected_vols[i], vol)
if expected_dists[i] != 0:
assert_almost_equal(expected_dists[i], dist)
assert_equal(i, 3)
for i, (vol, dist, surf) in enumerate(
dagmc.ray_iterator(startvol, start, direction, dist_limit=4)):
assert_equal(expected_vols[i], vol)
if expected_dists[i] != 0:
assert_almost_equal(expected_dists[i], dist)
assert_equal(i, 1)
def util_graveyard_bound():
from pyne import dagmc
dagmc.load(path)
lo, hi = dagmc.find_graveyard_inner_box()
return [lo, hi]
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"
# Load dagmc geometry
dagmc.load(hdf5)
bounds = [-5.0, 0.0, 5.0]
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 versions():
from pyne import dagmc
dagmc.load(path)
returned = dagmc.versions()
assert_equal(len(returned), 2)
assert_true(isinstance(returned[0], STRING_TYPES))
assert_true(isinstance(returned[1], int))
def boundary():
from pyne import dagmc
dagmc.load(path)
low, high = dagmc.volume_boundary(2)
for i in range(0, 3):
assert_true(low[i] <= -1.0)
assert_true(high[i] >= 1.0)
def boundary():
from pyne import dagmc
dagmc.load(path)
low, high = dagmc.volume_boundary(2)
for i in range(0, 3):
assert_true(low[i] <= -1.0)
assert_true(high[i] >= 1.0)
def list_functions():
from pyne import dagmc
dagmc.load(path)
surfs = dagmc.get_surface_list()
vols = dagmc.get_volume_list()
return [surfs, vols]
def util_matlist():
from pyne import dagmc
dagmc.load(path)
mats1 = dagmc.get_material_set()
mats2 = dagmc.get_material_set(with_rho=True)
return [mats1, mats2]
def discretize_non_square():
from pyne import dagmc
dagmc.load(path)
coords = [0, 1]
mesh = Mesh(structured=True,
structured_coords=[coords, coords, coords])
assert_raises(ValueError, dagmc.discretize_geom, mesh, num_rays=3, grid=True)
def versions():
from pyne import dagmc
dagmc.load(path)
returned = dagmc.versions()
assert_equal(len(returned), 2)
assert_true(isinstance(returned[0], STRING_TYPES))
assert_true(isinstance(returned[1], int))
def list_functions():
from pyne import dagmc
dagmc.load(path)
surfs = dagmc.get_surface_list()
assert_equal(set(surfs), set(range(1, 19)))
vols = dagmc.get_volume_list()
assert_equal(set(vols), set(range(1, 5)))
def metadata():
from pyne import dagmc
dagmc.load(path)
rets1 = [dagmc.volume_is_graveyard(x) for x in range(1, 5)]
rets2 = [dagmc.volume_is_implicit_complement(x) for x in range(1, 5)]
md = dagmc.volume_metadata(2)
return [rets1, rets2, md]
def discretize_geom_grid():
from pyne import dagmc
dagmc.load(path)
coords = [-4, -1, 1, 4]
mesh = Mesh(structured=True, structured_coords=[coords, coords, coords])
results = dagmc.discretize_geom(mesh, num_rays=49, grid=True)
return [results, coords]
def util_matlist():
from pyne import dagmc
dagmc.load(path)
mats = dagmc.get_material_set()
assert_equal(set((0, 5)), mats)
mats = dagmc.get_material_set(with_rho=True)
assert_equal(set([(0, 0.0), (5, 0.5)]), mats)
def cells_at_ve_centers():
from pyne import dagmc
dagmc.load(path)
coords = [0, 1]
coords2 = [0, 2, 4]
mesh = Mesh(structured=True, structured_coords=[coords2, coords, coords])
cells = dagmc.cells_at_ve_centers(mesh)
assert_array_equal(cells, [2, 3])
def list_functions():
from pyne import dagmc
dagmc.load(path)
surfs = dagmc.get_surface_list()
assert_equal(set(surfs), set(range(1, 19)))
vols = dagmc.get_volume_list()
assert_equal(set(vols), set(range(1, 5)))
def util_matlist():
from pyne import dagmc
dagmc.load(path)
mats = dagmc.get_material_set()
assert_equal(set((0, 5)), mats)
mats = dagmc.get_material_set(with_rho=True)
assert_equal(set([(0, 0.0), (5, 0.5)]), mats)
def step1():
config = ConfigParser.ConfigParser()
config.read(config_filename)
structured = config.getboolean("general", "structured")
meshtal = config.get("step1", "meshtal")
tally_num = config.getint("step1", "tally_num")
flux_tag = config.get("step1", "flux_tag")
decay_times = config.get("step2", "decay_times").split(",")
geom = config.get("step1", "geom")
reverse = config.getboolean("step1", "reverse")
num_rays = config.getint("step1", "num_rays")
grid = config.getboolean("step1", "grid")
responses = config.get("general", "responses").split(",")
wdr_file = config.get("general", "wdr_file")
load(geom)
# get meshtal info from meshtal file
flux_mesh = resolve_mesh(meshtal, tally_num, flux_tag)
# create the cell_fracs array before irradiation_steup
if flux_mesh.structured:
cell_fracs = discretize_geom(flux_mesh, num_rays=num_rays, grid=grid)
else:
cell_fracs = discretize_geom(flux_mesh)
cell_mats = cell_materials(geom)
irradiation_setup(
flux_mesh,
cell_mats,
cell_fracs,
alara_params_filename,
tally_num,
num_rays=num_rays,
grid=grid,
reverse=reverse,
output_mesh="activation_responses_step1.h5m",
flux_tag=flux_tag,
decay_times=decay_times,
sub_voxel=False,
responses=responses,
wdr_file=wdr_file,
)
# create a blank mesh for step 2:
ves = list(flux_mesh.iter_ve())
for tag in flux_mesh.get_all_tags():
tag.delete()
flux_mesh.write_hdf5("blank_mesh.h5m")
print("The file blank_mesh.h5m has been saved to disk.")
print(
"Do not delete this file; it is needed by activation_responses.py step2.\n"
)
print("Decay_heat step1 complete, run ALARA with the command:")
print(">> alara alara_inp > output.txt")
def ray_story():
from pyne import dagmc
dagmc.load(path)
# Run with `nosetests -s` to see output printed on stdout
dagmc.tell_ray_story((0, 0, 0), (1, 1, 0))
dagmc.tell_ray_story((-3, 0, 0), (1, 0, 0))
# tests edge behavior
dagmc.tell_ray_story((-3, 0, 0), (1, 0, 0), dist_limit=4)
dagmc.tell_ray_story((-3, 0, 0), (1, 0, 0), dist_limit=4.1)
def util_graveyard_bound():
from pyne import dagmc
dagmc.load(path)
lo, hi = dagmc.find_graveyard_inner_box()
grave_diam = 4.15692194
for i in range(0, 3):
assert_almost_equal(lo[i], -grave_diam)
assert_almost_equal(hi[i], grave_diam)
def cells_at_ve_centers():
from pyne import dagmc
dagmc.load(path)
coords = [0, 1]
coords2 = [0, 2, 4]
mesh = Mesh(structured=True, structured_coords=[coords2, coords, coords])
cells = dagmc.cells_at_ve_centers(mesh)
return cells
def cells_at_ve_centers():
from pyne import dagmc
dagmc.load(path)
coords = [0, 1]
coords2 = [0, 2, 4]
mesh = Mesh(structured=True,
structured_coords=[coords2, coords, coords])
cells = dagmc.cells_at_ve_centers(mesh)
assert_array_equal(cells, [2, 3])
def ray_story():
from pyne import dagmc
dagmc.load(path)
# Run with `nosetests -s` to see output printed on stdout
dagmc.tell_ray_story((0, 0, 0), (1, 1, 0))
dagmc.tell_ray_story((-3, 0, 0), (1, 0, 0))
# tests edge behavior
dagmc.tell_ray_story((-3, 0, 0), (1, 0, 0), dist_limit=4)
dagmc.tell_ray_story((-3, 0, 0), (1, 0, 0), dist_limit=4.1)
def util_graveyard_bound():
from pyne import dagmc
dagmc.load(path)
lo, hi = dagmc.find_graveyard_inner_box()
grave_diam = 4.15692194
for i in range(0, 3):
assert_almost_equal(lo[i], -grave_diam)
assert_almost_equal(hi[i], grave_diam)
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 step1():
config = ConfigParser.ConfigParser()
config.read(config_filename)
structured = config.getboolean('general', 'structured')
sub_voxel = config.getboolean('general', 'sub_voxel')
meshtal = config.get('step1', 'meshtal')
tally_num = config.getint('step1', 'tally_num')
flux_tag = config.get('step1', 'flux_tag')
decay_times = config.get('step2', 'decay_times').split(',')
geom = config.get('step1', 'geom')
reverse = config.getboolean('step1', 'reverse')
num_rays = config.getint('step1', 'num_rays')
grid = config.getboolean('step1', 'grid')
load(geom)
# get meshtal info from meshtal file
flux_mesh = resolve_mesh(meshtal, tally_num, flux_tag)
# create the cell_fracs array before irradiation_steup
if flux_mesh.structured:
cell_fracs = discretize_geom(flux_mesh, num_rays=num_rays, grid=grid)
# tag cell fracs for both default and subvoxel r2s modes
flux_mesh.tag_cell_fracs(cell_fracs)
else:
cell_fracs = discretize_geom(flux_mesh)
cell_mats = cell_materials(geom)
irradiation_setup(flux_mesh,
cell_mats,
cell_fracs,
alara_params_filename,
tally_num,
num_rays=num_rays,
grid=grid,
reverse=reverse,
flux_tag=flux_tag,
decay_times=decay_times,
sub_voxel=sub_voxel)
# create a blank mesh for step 2:
ves = list(flux_mesh.iter_ve())
tags_keep = ("cell_number", "cell_fracs", "cell_largest_frac_number",
"cell_largest_frac")
for tag in flux_mesh.get_all_tags():
if tag.name not in tags_keep and isinstance(tag, NativeMeshTag):
tag.delete()
flux_mesh.write_hdf5('blank_mesh.h5m')
print('The file blank_mesh.h5m has been saved to disk.')
print('Do not delete this file; it is needed by r2s.py step2.\n')
print('R2S step1 complete, run ALARA with the command:')
print('>> alara alara_inp > output.txt')
def pt_in_vol():
from pyne import dagmc
dagmc.load(path)
# there are 4 volumes; (0,0,.2) is in volume 2
rets = [dagmc.point_in_volume(x, [0, 0, .2]) for x in range(1, 5)]
assert_equal(rets, [False, True, False, False])
# (1.1,0,0) is in volume 3
rets = [dagmc.point_in_volume(x, [1.1, 0, 0]) for x in range(1, 5)]
assert_equal(rets, [False, False, True, False])
def pt_in_vol():
from pyne import dagmc
dagmc.load(path)
# there are 4 volumes; (0,0,.2) is in volume 2
rets = [dagmc.point_in_volume(x, [0, 0, .2]) for x in range(1, 5)]
assert_equal(rets, [False, True, False, False])
# (1.1,0,0) is in volume 3
rets = [dagmc.point_in_volume(x, [1.1, 0, 0]) for x in range(1, 5)]
assert_equal(rets, [False, False, True, False])
def discretize_non_square():
from pyne import dagmc
dagmc.load(path)
coords = [0, 1]
mesh = Mesh(structured=True, structured_coords=[coords, coords, coords])
assert_raises(ValueError,
dagmc.discretize_geom,
mesh,
num_rays=3,
grid=True)
def pt_in_vol():
from pyne import dagmc
dagmc.load(path)
# there are 4 volumes; (0,0,.2) is in volume 2
rets1 = [dagmc.point_in_volume(x, [0, 0, .2]) for x in range(1, 5)]
# (1.1,0,0) is in volume 3
rets2 = [dagmc.point_in_volume(x, [1.1, 0, 0]) for x in range(1, 5)]
return [rets1, rets2]
def failures():
from pyne import dagmc
dagmc.load(path)
# if Exception is raised, then None is returned, else nothing is returned
# and test will fail
i = assert_raises(Exception, dagmc.point_in_volume, [100, (0, 0, 0)])
j = assert_raises(Exception, dagmc.point_in_volume, [1, (0, 0, 0, 0)])
k = assert_raises(Exception, dagmc.fire_one_ray, [2, (0, 0, 0), 1])
return [i, j, k]
def step1():
config = ConfigParser.ConfigParser()
config.read(config_filename)
structured = config.getboolean('general', 'structured')
meshtal = config.get('step1', 'meshtal')
tally_num = config.getint('step1', 'tally_num')
flux_tag = config.get('step1', 'flux_tag')
decay_times = config.get('step2', 'decay_times').split(',')
geom = config.get('step1', 'geom')
reverse = config.getboolean('step1', 'reverse')
num_rays = config.getint('step1', 'num_rays')
grid = config.getboolean('step1', 'grid')
responses = config.get('general', 'responses').split(',')
wdr_file = config.get('general', 'wdr_file')
load(geom)
# get meshtal info from meshtal file
flux_mesh = resolve_mesh(meshtal, tally_num, flux_tag)
# create the cell_fracs array before irradiation_steup
if flux_mesh.structured:
cell_fracs = discretize_geom(flux_mesh, num_rays=num_rays, grid=grid)
else:
cell_fracs = discretize_geom(flux_mesh)
cell_mats = cell_materials(geom)
irradiation_setup(flux_mesh,
cell_mats,
cell_fracs,
alara_params_filename,
tally_num,
num_rays=num_rays,
grid=grid,
reverse=reverse,
output_mesh="activation_responses_step1.h5m",
flux_tag=flux_tag,
decay_times=decay_times,
sub_voxel=False,
responses=responses,
wdr_file=wdr_file)
# create a blank mesh for step 2:
ves = list(flux_mesh.iter_ve())
for tag in flux_mesh.get_all_tags():
tag.delete()
flux_mesh.write_hdf5('blank_mesh.h5m')
print('The file blank_mesh.h5m has been saved to disk.')
print(
'Do not delete this file; it is needed by activation_responses.py step2.\n'
)
print('Decay_heat step1 complete, run ALARA with the command:')
print('>> alara alara_inp > output.txt')
def discretize_geom_mix():
from pyne import dagmc
dagmc.load(path)
coords = [0, 1]
coords2 = [0, 2]
mesh = Mesh(structured=True, structured_coords=[coords2, coords, coords])
results1 = dagmc.discretize_geom(mesh, num_rays=100, grid=True)
# To to make sure standard error decreases with increasing rays
results2 = dagmc.discretize_geom(mesh, num_rays=625, grid=True)
return [results1, results2]
def metadata():
from pyne import dagmc
dagmc.load(path)
rets = [dagmc.volume_is_graveyard(x) for x in range(1, 5)]
assert_equal(rets, [True, False, False, False])
rets = [dagmc.volume_is_implicit_complement(x) for x in range(1, 5)]
assert_equal(rets, [False, False, False, True])
md = dagmc.volume_metadata(2)
assert_equal(md['material'], 5)
assert_equal(md['rho'], 0.5)
assert_true(all(x in md for x in ['material', 'rho', 'imp']))
def discretize_geom_grid():
from pyne import dagmc
dagmc.load(path)
coords = [-4, -1, 1, 4]
mesh = Mesh(structured=True, structured_coords=[coords, coords, coords])
results = dagmc.discretize_geom(mesh, num_rays=49, grid=True)
assert_equal(len(results), (len(coords) - 1)**3)
for res in results:
if res['idx'] != 13:
assert_equal(res['cell'], 3)
else:
assert_equal(res['cell'], 2)
assert_almost_equal(res['vol_frac'], 1.0)
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 get_zones_with_void():
"""Test the _get_zones function if a void is present.
"""
# 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'
from pyne import dagmc
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
voxel_zones, zones = partisn._get_zones(mesh, hdf5, bounds, num_rays, grid)
# 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'HeliumNatural']},
2:{'vol_frac':[0.5, 0.5], 'mat':[u'HeliumNatural', u'Mercury']},
3:{'vol_frac':[1.0], 'mat':[u'Mercury']}}
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 discretize_geom_mix():
from pyne import dagmc
dagmc.load(path)
coords = [0, 1]
coords2 = [0, 2]
mesh = Mesh(structured=True,
structured_coords=[coords2, coords, coords])
results1 = dagmc.discretize_geom(mesh, num_rays=100, grid=True)
assert_equal(results1[0]['cell'], 2)
assert_almost_equal(results1[0]['vol_frac'], 0.5)
assert_equal(results1[1]['cell'], 3)
assert_almost_equal(results1[1]['vol_frac'], 0.5)
# To to make sure standard error decreases with increasing rays
results2 = dagmc.discretize_geom(mesh, num_rays=625, grid=True)
assert(results2[0]['rel_error'] < results1[0]['rel_error'])
assert(results2[1]['rel_error'] < results1[1]['rel_error'])
def one_ray():
from pyne import dagmc
dagmc.load(path)
fromcenter = dagmc.fire_one_ray(2, [0, 0, 0], [1, 0, 0])
assert_almost_equal(fromcenter[1], 1.0)
fromhalf = dagmc.fire_one_ray(2, [.5, .5, .5], [0, -1, 0])
assert_almost_equal(fromhalf[1], 1.5)
# the following is actually a misuse of ray_fire because it should only
# be called from inside a volume, but at least verify that a ray is
# lost if it 1) starts outside a volume and 2) does not intersect the
# volume
fromoutside = dagmc.fire_one_ray(2, [0, 1.1, 0], [-1, 0, 0])
assert_equal(fromoutside, None)
fromvol3 = dagmc.fire_one_ray(3, [0, 1.1, 0], [0, -1, 0])
assert_almost_equal(fromvol3[1], 0.1)
fromvol3 = dagmc.fire_one_ray(3, [0, 1.1, 0], [0, 1, 0])
assert_almost_equal(fromvol3[1], 3.056921938)
def find_volume():
from pyne import dagmc
dagmc.load(path)
vol = dagmc.find_volume([0, 0, 0])
assert_equal(vol, 2)
vol = dagmc.find_volume([.9, .9, .9])
assert_equal(vol, 2)
# boundary case -- point [1,.1,.1] is on surface between vols 2 and 3
# the behavior on boundaries will vary with uvw, but ensure that
# only the two volumes the touch the location are ever returned.
for uvw in [(1, 0, 0), (-1, 0, 0), (0, 1, 0), (0, -1, 0)]:
vol = dagmc.find_volume([1, .1, .1], uvw)
assert_true(vol in (2, 3))
# boundary case-- exiting volume 3 => in volume 3
vol = dagmc.find_volume([1, .1, .1], [-1, 0, 0])
assert_equal(vol, 3)
vol = dagmc.find_volume([1.1, 0, 0])
assert_equal(vol, 3)
def load():
from pyne import dagmc
# FIXME laoding causes infor to be printied to stderr (or stdout).
dagmc.load(path)
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 _get_zones(mesh, hdf5, bounds, num_rays, grid):
"""Get the minimum zone definitions for the geometry.
"""
# load the geometry
from pyne import dagmc
dagmc.load(hdf5)
# Descretize the geometry and get cell fractions
dg = dagmc.discretize_geom(mesh, num_rays=num_rays, grid=grid)
# Reorganize dictionary of each voxel's info with the key the voxel number
# and values of cell and volume fraction
voxel = {}
for i in dg:
idx = i[0] # voxel number
if idx not in voxel:
voxel[idx] = {}
voxel[idx]['cell'] = []
voxel[idx]['vol_frac'] = []
voxel[idx]['cell'].append(i[1])
voxel[idx]['vol_frac'].append(i[2])
# get material to cell assignments
mat_assigns = dagmc.cell_material_assignments(hdf5)
# Replace cell numbers with materials, eliminating duplicate materials
# within single zone definition
zones = {}
for z in voxel:
zones[z] = {}
zones[z]['vol_frac'] = []
zones[z]['mat'] = []
for i, cell in enumerate(voxel[z]['cell']):
if mat_assigns[cell] not in zones[z]['mat']:
# create new entry
zones[z]['mat'].append(mat_assigns[cell])
zones[z]['vol_frac'].append(voxel[z]['vol_frac'][i])
else:
# update value that already exists with new volume fraction
for j, val in enumerate(zones[z]['mat']):
if mat_assigns[cell] == val:
vol_frac = zones[z]['vol_frac'][j] + voxel[z]['vol_frac'][i]
zones[z]['vol_frac'][j] = vol_frac
# Remove vacuum or graveyard from material definition if not vol_frac of 1.0
skip_array = [['mat:Vacuum'], ['mat:vacuum'], ['mat:Graveyard'], ['mat:graveyard']]
skip_list = ['mat:Vacuum', 'mat:vacuum', 'mat:Graveyard', 'mat:graveyard']
zones_compressed = {}
for z, info in zones.iteritems():
# check first if the definition is 100% void, keep same if is
if zones[z]['mat'] in skip_array and zones[z]['vol_frac'] == [1.0]:
zones_compressed[z] = info
else:
# check for partial void
zones_compressed[z] = {'mat':[], 'vol_frac':[]}
for i, mat in enumerate(zones[z]['mat']):
if mat not in skip_list:
zones_compressed[z]['mat'].append(mat)
zones_compressed[z]['vol_frac'].append(zones[z]['vol_frac'][i])
# Eliminate duplicate zones and assign each voxel a zone number.
# Assign zone = 0 if vacuum or graveyard and eliminate material definition.
voxel_zone = {}
zones_mats = {}
z = 0
match = False
first = True
for i, vals in zones_compressed.iteritems():
# Find if the zone already exists
for zone, info in zones_mats.iteritems():
# Iterate through both sets to disregard order
match_all = np.empty(len(vals['mat']), dtype=bool)
match_all.fill(False)
for ii, mat in enumerate(vals['mat']):
for jj, mat_info in enumerate(info['mat']):
if mat == mat_info and np.allclose(np.array(vals['vol_frac'][ii]), \
np.array(info['vol_frac'][jj]), rtol=1e-5):
match_all[ii] = True
break
if match_all.all() == True:
match = True
y = zone
break
else:
match = False
# Create a new zone if first zone or does not match other zones
if first or not match:
# Check that the material is not 100% void (assign zone 0 otherwise)
if vals['mat'] in skip_array:
voxel_zone[i] = 0
else:
z += 1
zones_mats[z] = zones_compressed[i]
voxel_zone[i] = z
first = False
else:
if vals['mat'] in skip_array:
voxel_zone[i] = 0
else:
voxel_zone[i] = y
# Remove any instances of graveyard or vacuum in zone definitions
zones_novoid = {}
for z in zones_mats:
zones_novoid[z] = {'mat':[], 'vol_frac':[]}
for i, mat in enumerate(zones_mats[z]['mat']):
if mat not in skip_list:
name = strip_mat_name(mat)
zones_novoid[z]['mat'].append(name)
zones_novoid[z]['vol_frac'].append(zones_mats[z]['vol_frac'][i])
# Put zones into format for PARTISN input
if 'x' in bounds:
im = len(bounds['x']) - 1
else:
im = 1
if 'y' in bounds:
jm = len(bounds['y']) - 1
else:
jm = 1
if 'z' in bounds:
km = len(bounds['z']) - 1
else:
km = 1
n = 0
zones_formatted = np.zeros(shape=(jm*km, im), dtype=int)
for i in range(im):
for jk in range(jm*km):
zones_formatted[jk, i] = voxel_zone[n]
n += 1
return zones_formatted, zones_novoid
def test__load(self):
# FIXME laoding causes infor to be printied to stderr (or stdout).
path = os.path.join(os.path.dirname(__file__), 'unitbox.h5m')
dagmc.load(path)
vector.append(float(split_str[5]))
direction.append(vector)
# speed
speed.append(float(split_str[6]))
return xyz,direction,speed
(xyz,direction,speed) = load_input_file("input.txt")
mesh = Mesh(mesh="../geom/conv_pipe_mesh.h5m")
# load dag geometry
load("../geom/conv_pipe_geom.h5m")
# discretise geom onto mesh
cell_fracs = discretize_geom(mesh)
mesh.vol_id = IMeshTag(1,int)
mesh.source_strength = IMeshTag(1,float)
id_list = []
for element in cell_fracs:
id_list.append(element["cell"])
mesh.vol_id[:]=id_list
# loop along path, use point in volume to determine the vol id
volumes = get_all_cells(xyz,direction,speed)