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 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 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, metadata={'mat_number': 11}),
3:
Material({
3007: 0.4,
3006: 0.6
},
density=2.0,
metadata={'mat_number': 12})
}
alara_params = "Bogus line for testing\n"
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")
output_material = True
irradiation_setup(meshtal, cell_mats, alara_params, tally_num, geom,
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)
m_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]
]
os.remove(alara_inp)
os.remove(alara_matlib)
os.remove(fluxin)
os.remove(output_mesh)
return [m_out, f1, f2, f3]
def 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, metadata={'mat_number':11}),
3: Material({3007: 0.4, 3006: 0.6}, density=2.0, metadata={'mat_number':12})}
alara_params = "Bogus line for testing\n"
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")
output_material = True
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,
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)
m_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]]
os.remove(meshtal_mesh_file)
os.remove(alara_inp)
os.remove(alara_matlib)
os.remove(fluxin)
os.remove(output_mesh)
return [m_out, f1, f2, f3]
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 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 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, metadata={'mat_number': 11}),
3: Material({3007: 0.4, 3006: 0.6}, density=2.0, metadata={'mat_number':12})}
alara_params = "Bogus line for testing\n"
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")
output_material = True
irradiation_setup(meshtal, cell_mats, alara_params, tally_num, geom,
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)
m_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]]
os.remove(alara_inp)
os.remove(alara_matlib)
os.remove(fluxin)
os.remove(output_mesh)
return [m_out, f1, f2, f3]
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)
m_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]
]
os.remove(alara_inp)
os.remove(alara_matlib)
os.remove(fluxin)
os.remove(output_mesh)
return [m_out, f1, f2, f3]
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)
m_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]
]
os.remove(meshtal_mesh_file)
os.remove(alara_inp)
os.remove(alara_matlib)
os.remove(fluxin)
os.remove(output_mesh)
return [m_out, f1, f2, f3]
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_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)
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 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_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, metadata={'mat_number': 11}),
3:
Material({
3007: 0.4,
3006: 0.6
},
density=2.0,
metadata={'mat_number': 12})
}
alara_params = "Bogus line for testing\n"
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")
output_material = True
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,
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)
m_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]
]
os.remove(meshtal_mesh_file)
os.remove(alara_inp)
os.remove(alara_matlib)
os.remove(fluxin)
os.remove(output_mesh)
return [m_out, f1, f2, f3]
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_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)