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 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 step2():
config = ConfigParser.ConfigParser()
config.read(config_filename)
structured = config.getboolean("general", "structured")
sub_voxel = config.getboolean("general", "sub_voxel")
decay_times = config.get("step2", "decay_times").split(",")
output = config.get("step2", "output")
tot_phtn_src_intensities = config.get("step2", "tot_phtn_src_intensities")
tag_name = "source_density"
if sub_voxel:
geom = config.get("step1", "geom")
load(geom)
cell_mats = cell_materials(geom)
else:
cell_mats = None
h5_file = "phtn_src.h5"
if not isfile(h5_file):
photon_source_to_hdf5(filename="phtn_src", nucs="total")
intensities = "Total photon source intensities (p/s)\n"
e_bounds = phtn_src_energy_bounds("alara_inp")
for i in range(len(e_bounds)):
e_bounds[i] /= 1.0e6 # convert unit from eV to MeV
for i, dt in enumerate(decay_times):
print("Writing source for decay time: {0} to mesh".format(dt))
mesh = Mesh(structured=structured, mesh="blank_mesh.h5m")
tags = {("TOTAL", dt): tag_name}
photon_source_hdf5_to_mesh(mesh,
h5_file,
tags,
sub_voxel=sub_voxel,
cell_mats=cell_mats)
p_src_filename = "{0}_{1}.h5m".format(output, i + 1)
intensity = total_photon_source_intensity(mesh,
tag_name,
sub_voxel=sub_voxel)
mesh = tag_e_bounds(mesh, e_bounds)
mesh = tag_source_intensity(mesh, intensity)
# get and tag decay time
decay_time = to_sec(float(dt.split()[0]), dt.split()[1])
mesh = tag_decay_time(mesh, decay_time)
# set version manually when changing the information of source.h5m
mesh = tag_version(mesh)
mesh.write_hdf5("{0}_{1}.h5m".format(output, i + 1))
intensities += "{0}: {1}\n".format(dt, intensity)
with open(tot_phtn_src_intensities, "w") as f:
f.write(intensities)
print("R2S step2 complete.")
def step2():
config = ConfigParser.ConfigParser()
config.read(config_filename)
structured = config.getboolean('general', 'structured')
sub_voxel = config.getboolean('general', 'sub_voxel')
decay_times = config.get('step2', 'decay_times').split(',')
output = config.get('step2', 'output')
tot_phtn_src_intensities = config.get('step2', 'tot_phtn_src_intensities')
tag_name = "source_density"
if sub_voxel:
geom = config.get('step1', 'geom')
load(geom)
cell_mats = cell_materials(geom)
else:
cell_mats = None
h5_file = 'phtn_src.h5'
if not isfile(h5_file):
photon_source_to_hdf5('phtn_src')
intensities = "Total photon source intensities (p/s)\n"
for i, dc in enumerate(decay_times):
print('Writing source for decay time: {0}'.format(dc))
mesh = Mesh(structured=structured, mesh='blank_mesh.h5m')
tags = {('TOTAL', dc): tag_name}
photon_source_hdf5_to_mesh(mesh,
h5_file,
tags,
sub_voxel=sub_voxel,
cell_mats=cell_mats)
mesh.write_hdf5('{0}_{1}.h5m'.format(output, i + 1))
intensity = total_photon_source_intensity(mesh,
tag_name,
sub_voxel=sub_voxel)
intensities += "{0}: {1}\n".format(dc, intensity)
with open(tot_phtn_src_intensities, 'w') as f:
f.write(intensities)
e_bounds = phtn_src_energy_bounds("alara_inp")
e_bounds_str = ""
for e in e_bounds:
e = e / 1e6 # convert unit to MeV
e_bounds_str += "{0}\n".format(e)
with open("e_bounds", 'w') as f:
f.write(e_bounds_str)
print('R2S step2 complete.')
def step2():
config = ConfigParser.ConfigParser()
config.read(config_filename)
structured = config.getboolean('general', 'structured')
sub_voxel = config.getboolean('general', 'sub_voxel')
decay_times = config.get('step2', 'decay_times').split(',')
output = config.get('step2', 'output')
tot_phtn_src_intensities = config.get('step2', 'tot_phtn_src_intensities')
tag_name = "source_density"
if sub_voxel:
geom = config.get('step1', 'geom')
load(geom)
cell_mats = cell_materials(geom)
else:
cell_mats = None
h5_file = 'phtn_src.h5'
if not isfile(h5_file):
photon_source_to_hdf5(filename='phtn_src', nucs='total')
intensities = "Total photon source intensities (p/s)\n"
e_bounds = phtn_src_energy_bounds("alara_inp")
for i in range(len(e_bounds)):
e_bounds[i] /= 1.0e6 # convert unit from eV to MeV
for i, dt in enumerate(decay_times):
print('Writing source for decay time: {0} to mesh'.format(dt))
mesh = Mesh(structured=structured, mesh='blank_mesh.h5m')
tags = {('TOTAL', dt): tag_name}
photon_source_hdf5_to_mesh(mesh, h5_file, tags, sub_voxel=sub_voxel,
cell_mats=cell_mats)
intensity = total_photon_source_intensity(mesh, tag_name,
sub_voxel=sub_voxel)
mesh = tag_e_bounds(mesh, e_bounds)
mesh = tag_source_intensity(mesh, intensity)
# get and tag decay time
decay_time = to_sec(float(dt.split()[0]), dt.split()[1])
mesh = tag_decay_time(mesh, decay_time)
# set version manually when changing the information of source.h5m
mesh = tag_version(mesh)
mesh.write_hdf5('{0}_{1}.h5m'.format(output, i+1))
intensities += "{0}: {1}\n".format(dt, intensity)
with open(tot_phtn_src_intensities, 'w') as f:
f.write(intensities)
print('R2S step2 complete.')
def cell_materials():
from pyne import dagmc
path = os.path.join(os.path.dirname(__file__), 'files_test_dagmc',
'three_blocks.h5m')
c = dagmc.cell_materials(path)
r = []
r.append(c[1].comp == {10010000: 1.0})
r.append(c[1].density == 1.0)
r.append(c[1].metadata['name'] == 'mat:m1/rho:1.0')
r.append(c[2].comp == {20040000: 1.0})
r.append(c[2].density == 2.0)
r.append(c[2].metadata['name'] == 'mat:m2')
r.append(c[3].comp == {20040000: 1.0})
r.append(c[3].density == 3.0)
r.append(c[3].metadata['name'] == 'mat:m2/rho:3.0')
r.append(c[6].comp == {})
r.append(c[6].density == 0)
r.append(c[6].metadata['name'] == 'void')
return np.all(r)
def cell_materials():
from pyne import dagmc
path = os.path.join(os.path.dirname(__file__), "files_test_dagmc",
"three_blocks.h5m")
c = dagmc.cell_materials(path)
r = []
r.append(c[1].comp == {10010000: 1.0})
r.append(c[1].density == 1.0)
r.append(c[1].metadata["name"] == "mat:m1/rho:1.0")
r.append(c[2].comp == {20040000: 1.0})
r.append(c[2].density == 2.0)
r.append(c[2].metadata["name"] == "mat:m2")
r.append(c[3].comp == {20040000: 1.0})
r.append(c[3].density == 3.0)
r.append(c[3].metadata["name"] == "mat:m2/rho:3.0")
r.append(c[6].comp == {})
r.append(c[6].density == 0)
r.append(c[6].metadata["name"] == "void")
return np.all(r)
