def cell_material_assignments():
from pyne import dagmc
path = os.path.join(os.path.dirname(__file__), 'files_test_dagmc',
'three_blocks.h5m')
c = dagmc.cell_material_assignments(path)
r = []
r.append(c[1] == 'mat:m1/rho:1.0')
r.append(c[2] == 'mat:m2')
r.append(c[3] == 'mat:m2/rho:3.0')
r.append(c[6] == 'mat:graveyard')
return np.all(r)
def _get_zones(mesh, hdf5, bounds, num_rays, grid, dg, mat_assigns,
unique_names):
"""Get the minimum zone definitions for the geometry."""
# Discretize the geometry and get cell fractions
if dg is None:
if not HAVE_DAGMC:
raise RuntimeError("DAGMC is not available."
"Unable to discretize the geometry.")
else:
dagmc.load(hdf5)
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
if mat_assigns is None:
if not HAVE_DAGMC:
raise RuntimeError("DAGMC is not available."
"Unable to get cell material assignments.")
else:
mat_assigns = dagmc.cell_material_assignments(hdf5)
# Replace the names in the material assignments with unique names
temp = {}
for i, name in mat_assigns.items():
if "vacuum" in name.lower() or "graveyard" in name.lower():
temp[i] = name
else:
temp[i] = unique_names[name]
mat_assigns = temp
# 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.items():
# 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.items():
# Find if the zone already exists
for zone, info in zones_mats.items():
# 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:
zones_novoid[z]["mat"].append(mat)
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):
temp = np.zeros(shape=(jm * km), dtype=int)
for jk in range(jm * km):
temp[jk] = voxel_zone[n]
n += 1
temp = np.reshape(temp, (jm, km))
temp = np.transpose(temp)
temp = np.reshape(temp, jm * km)
zones_formatted[:, i] = temp
return zones_formatted, zones_novoid
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 step5(cfg, cfg2, cfg5):
"""
This function creates the adjoint neutron source and writes the
PARTISN input file for adjoint neutron transport.
Parameters
----------
cfg : dictionary
User input from 'general' section of config.yml file
cfg2 : dictionary
User input for step 2 from the config.yml file
cfg5 : dictionary
User input for step 3 from the config.yml file
"""
# Get user-input from config file
num_n_groups = cfg['n_groups']
num_p_groups = cfg['p_groups']
n_geom = cfg2['n_geom_file']
decay_times = str(cfg2['decay_times']).split(' ')
meshflux = cfg5['meshflux']
# Base of geometry file name
basename = n_geom.split("/")[-1].split(".")[0]
# The total number of photon and neutron energy groups
total_num_groups = num_n_groups + num_p_groups
# Read given flux file and tag to a mesh
if meshflux:
# Adjoint flux file is an hdf5 mesh file
fw_n_err = meshflux
m = Mesh(structured=True, mesh=fw_n_err, mats=None)
else:
raise RuntimeError("No neutron flux file given")
# Size of flux tag is equal to the total number of energy groups
m.ERROR_TAG = NativeMeshTag(num_n_groups, name="ERROR_TAG")
fw_n_err = m.ERROR_TAG[:]
# Load geometry and get material assignments
load(n_geom)
ml = MaterialLibrary(n_geom)
mat_names = list(ml.keys())
cell_mats = cell_material_assignments(n_geom)
# Load T matrix
if not os.path.exists('step2_T.npy'):
raise RuntimeError("T matrix from step 2 (step2_T.npy) not found")
T = np.load('step2_T.npy')
# Loop over mesh voxels and calculate the error in the photon source by multiplying neutron flux and T matrix
dg = discretize_geom(m)
for t, dt in enumerate(decay_times):
temp = np.zeros(shape=(len(m), num_p_groups))
for i in range(len(m)):
for row in np.atleast_1d(dg[dg["idx"] == i]):
cell = row[1]
if not cell_mats[cell] in mat_names:
continue
vol_frac = row[2]
mat = mat_names.index(cell_mats[cell])
for h in range(num_p_groups):
for g in range(num_n_groups):
temp[i, h] += (fw_n_err[i, g]**2) * T[mat, t, g,
h] * vol_frac
print("err ", temp[i, h])
# Tag the mesh with the squared error in the photon source values
tag_name = "sq_err_q_src_{0}".format(dt)
m.err_q_src = NativeMeshTag(num_p_groups, name=tag_name)
m.err_q_src[:] = temp
# Save adjoint neutron source mesh file tagged with values for all decay times
m.save("sq_err_q_src.h5m")
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